Reagents and methods useful for detecting diseases of the breast

ABSTRACT

A set of contiguous and partially overlapping cDNA sequences and polypeptides encoded thereby, designated as BS249 and transcribed from breast tissue, is described. These sequences are useful for the detecting, diagnosing, staging, monitoring, prognosticating, in vivo imaging, preventing or treating, or determining the predisposition of an individual to diseases and conditions of the breast, such as breast cancer. Also provided are antibodies which specifically bind to BS249-encoded polypeptide or protein, and agonists or inhibitors which prevent action of the tissue-specific BS249 polypeptide, which molecules are useful for the therapeutic treatment of breast diseases, tumors or metastases

CROSS-REFERENCE TO RELATED APPLICATION

This application is a continuation-in-part of U.S. application Ser. No.08/972,940, filed Nov. 18, 1997, now abandoned, from which priority isclaimed pursuant to 35 U.S.C. §120 and which is incorporated herein byreference in its entirety.

BACKGROUND OF THE INVENTION

This invention relates generally to detecting diseases of the breast.Furthermore, the invention also relates to reagents and methods fordetecting diseases of the breast. More particularly, the presentinvention relates to reagents such as polynucleotide sequences and thepolypeptide sequences encoded thereby, as well as methods which utilizethese sequences. The polynucleotide and polypeptide sequences are usefulfor detecting, diagnosing, staging, monitoring, prognosticating, in vivoimaging, preventing or treating, or determining predisposition todiseases or conditions of the breast, such as breast cancer.

Breast cancer is the most common form of cancer occurring in females inthe U.S. The incidence of breast cancers in the United States isprojected to be 180,300 cases diagnosed and 43,900 breast cancer-relateddeaths to occur during 1998 (American Cancer Society statistics).Worldwide, the incidence of breast cancer increased from 700,000 in 1985to about 900,000 in 1990. G. N. Hortobagyi et al., CA Cancer J Clin45:199-226 (1995).

Procedures used for detecting, diagnosing, staging, monitoring,prognosticating, in vivo imaging, preventing or treating, or determiningpredisposition to diseases or conditions of the breast, such as breastcancer, are of critical importance to the outcome of the patient. Forexample, patients diagnosed with early breast cancer have greater than a90% five-year relative survival rate as compared to a survival rate ofabout 20% for patients diagnosed with distantly metastasized breastcancers. (American Cancer Society statistics). Currently, the bestinitial indicators of early breast cancer are physical examination ofthe breast and mammography. J. R. Harris et al. In: Cancer: Principlesand Practice of Oncology, Fourth Edition, pp. 1264-1332, Philadelphia,Pa.: J/B. Lippincott Co. (1993). Mammography may detect a breast tumorbefore it can be detected by physical examination, but it haslimitations. For example, mammography's predictive value depends on theobserver's skill and the quality of the mammogram. In addition, 80 to93% of suspicious mammograms are false positives, and 10 to 15% of womenwith breast cancer have false negative mammograms. C. J. Wright et al.,Lancet 346:29-32 (1995). New diagnostic methods which are more sensitiveand specific for detecting early breast cancer are clearly needed.

Breast cancer patients are closely monitored following initial therapyand during adjuvant therapy to determine response to therapy, and todetect persistent or recurrent disease, or early distant metastasis.Current diagnostic procedures for monitoring breast cancer includemammography, bone scan, chest radiographs, liver function tests andtests for serum markers. The serum tumor markers most commonly used formonitoring patients are carcinoembryonic antigen (CEA) and CA 15-3.Limitations of CEA include absence of elevated serum levels in about 40%of women with metastatic disease. In addition, CEA elevation duringadjuvant therapy may not be related to recurrence but to other factorsthat are not clinically important. CA 15-3 can also be negative in asignificant number of patients with progressive disease and, therefore,fail to predict metastasis. Both CEA and CA 15-3 can be elevated innonmalignant, benign conditions giving rise to false positive results.Therefore, it would be clinically beneficial to find a breast associatedmarker which is more sensitive and specific in detecting cancerrecurrence. J. R. Harris et al., supra. M. K. Schwartz, In: Cancer:Principles and Practice of Oncology, Vol. 1, Fourth Edition, pp.531-542, Philadelphia, Pa.: J/B. Lippincott Co. 1993.

Another important step in managing breast cancer is to determine thestage of the patient's disease because stage determination has potentialprognostic value and provides criteria for designing optimal therapy.Currently, pathological staging of breast cancer is preferable overclinical staging because the former gives a more accurate prognosis. J.R. Harris et al., supra. On the other hand, clinical staging would bepreferred were it at least as accurate as pathological staging becauseit does not depend on an invasive procedure to obtain tissue forpathological evaluation. Staging of breast cancer could be improved bydetecting new markers in serum or urine which could differentiatebetween different stages of invasion. Such markers could be MRNA orprotein markers expressed by cells originating from the primary tumor inthe breast but residing in blood, bone marrow or lymph nodes and couldserve as sensitive indicators for metastasis to these distal organs. Forexample, specific protein antigens and MRNA, associated with breastepithelial cells, have been detected by immunohistochemical techniquesand RT-PCR, respectively, in bone marrow, lymph nodes and blood ofbreast cancer patients suggesting metastasis. K. Pantel et al.,Onkologie 18:394-401 (1995).

Such diagnostic procedures also could include immunological assays basedupon the appearance of various disease markers in test samples such asblood, plasma, serum or urine obtained by minimally invasive procedureswhich are detectable by immunological methods. These diagnosticprocedures would provide information to aid the physician in managingthe patient with disease of the breast, at low cost to the patient.Markers such as prostate specific antigen (PSA) and human chorionicgonadotropin (hCG) exist and are used clinically for screening patientsfor prostate cancer and testicular cancer, respectively. For example,PSA normally is secreted by the prostate at high levels into the seminalfluid, but is present in very low levels in the blood of men with normalprostates. Elevated levels of PSA protein in serum are used in the earlydetection of prostate cancer or disease in asymptomatic men. See, forexample, G. E. Hanks et al., In: Cancer: Principles and Practice ofOncology, Vol. 1, Fourth Edition, pp. 1073-1113, Philadelphia, Pa.: J.B. Lippincott Co. 1993. M. K. Schwartz et al., In: Cancer: Principlesand Practice of Oncology, Vol. 1, Fourth Edition, pp. 531-542,Philadelphia, Pa.: J. B. Lippincott Co. 1993. Likewise, the managementof breast diseases could be improved by the use of new markers normallyexpressed in the breast but found in elevated amounts in aninappropriate body compartment as a result of the disease of the breast.

Further, new markers which could predict the biologic behavior of earlybreast cancers would also be of significant value. Early breast cancersthat threaten or will threaten the life of the patient are moreclinically important than those that do not or will not be a threat. G.E. Hanks, supra. Such markers are needed to predict which patients withhistologically negative lymph nodes will experience recurrence of cancerand also to predict which cases of ductal carcinoma in situ will developinto invasive breast carcinoma. More accurate prognostic markers wouldallow the clinician to accurately identify early cancers localized tothe breast which will progress and metastasize if not treatedaggressively. Additionally, the absence of a marker for an aggressivecancer in the patient could spare the patient expensive andnon-beneficial treatment. J. R. Harris et al., supra. E. R. Frykberg etal., Cancer 74:350-361 (1994).

It therefore would be advantageous to provide specific methods andreagents useful for detecting, diagnosing, staging, monitoring,prognosticating, in vivo imaging, preventing or treating, or determiningpredisposition to diseases or conditions of the breast. Such methodswould include assaying a test sample for products of a gene which areoverexpressed in diseases and conditions associated with the breast,including cancer. Such methods may also include assaying a test samplefor products of a gene which have been altered by the disease orcondition associated with the breast, including cancer. Such methods mayfurther include assaying a test sample for products of a gene whosedistribution among the various tissues and compartments of the body havebeen altered by a breast-associated disease or condition, includingcancer. Such methods would comprise making cDNA from mRNA in the testsample, amplifying, when necessary, portions of the cDNA correspondingto the gene or a fragment thereof, and detecting the cDNA product as anindication of the presence of the disease or condition including canceror detecting translation products of the niRNAs comprising genesequences as an indication of the presence of the disease. Usefulreagents include polynucleotide(s), or fragment(s) thereof which may beused in diagnostic methods such as reverse transcriptase-polymerasechain reaction (RT-PCR), PCR, or hybridization assays of mRNA extractedfrom biopsied tissue, blood or other test samples; or proteins which arethe translation products of such mRNAs; or antibodies directed againstthese proteins. Such assays would include methods for assaying a samplefor product(s) of the gene and detecting the product(s) as an indicationof disease of the breast. Drug treatment or gene therapy for diseasesand conditions of the breast including cancer can be based on theseidentified gene sequences or their expressed proteins, and efficacy ofany particular therapy can be monitored. Furthermore, it would beadvantageous to have available alternative, non-surgical diagnosticmethods capable of detecting early stage breast disease, such as cancer.

SUMMARY OF THE INVENTION

The present invention provides a method of detecting a target BS249polynucleotide in a test sample which comprises contacting the testsample with at least one BS249-specific polynucleotide and detecting thepresence of the target BS249 polynucleotide in the test sample. TheBS249-specific polynucleotide has at least 50% identity with apolynucleotide selected from the group consisting of SEQUENCE ID NO 1,SEQUENCE ID NO 2, SEQUENCE ID NO 3, SEQUENCE ID NO 4, SEQUENCE ID NO 5,SEQUENCE ID NO 6, SEQUENCE ID NO 7, SEQUENCE ID NO 8, SEQUENCE ID NO 9,SEQUENCE ID NO 10, SEQUENCE ID NO 11 (SEQUENCE ID NOS 1-11), andfragments or complements thereof. Also, the BS249-specificpolynucleotide may be attached to a solid phase prior to performing themethod.

The present invention also provides a method for detecting BS249 mRNA ina test sample, which comprises performing reverse transcription (RT)with at least one primer in order to produce cDNA, amplifying the cDNAso obtained using BS249 oligonucleotides as sense and antisense primersto obtain BS249 amplicon, and detecting the presence of the BS249amplicon as an indication of the presence of BS249 mRNA in the testsample, wherein the BS249 oligonucleotides have at least 50% identitywith a sequence selected from the group consisting of SEQUENCE ID NOS1-11, and fragments or complements thereof. Amplification can beperformed by the polymerase chain reaction. Also, the test sample can bereacted with a solid phase prior to performing the method, prior toamplification or prior to detection. This reaction can be a direct or anindirect reaction. Further, the detection step can comprise utilizing adetectable label capable of generating a measurable signal. Thedetectable label can be attached to a solid phase.

The present invention further provides a method of detecting a targetBS249 polynucleotide in a test sample suspected of containing targetBS249 polynucleotides, which comprises (a) contacting the test samplewith at least one BS249 oligonucleotide as a sense primer and at leastone BS249 oligonucleotide as an anti-sense primer, and amplifying sameto obtain a first stage reaction product; (b) contacting the first stagereaction product with at least one other BS249 oligonucleotide to obtaina second stage reaction product, with the proviso that the other BS249oligonucleotide is located 3′ to the BS249 oligonucleotides utilized instep (a) and is complementary to the first stage reaction product; and(c) detecting the second stage reaction product as an indication of thepresence of a target BS249 polynucleotide in the test sample. The BS249oligonucleotides selected as reagents in the method have at least 50%identity with a sequence selected from the group consisting of SEQUENCEID NOS 1-11, and fragments or complements thereof. Amplification may beperformed by the polymerase chain reaction. The test sample can bereacted either directly or indirectly with a solid phase prior toperforming the method, or prior to amplification, or prior to detection.The detection step also comprises utilizing a detectable label capableof generating a measurable signal; further, the detectable label can beattached to a solid phase.

Test kits useful for detecting target BS249 polynucleotide in a testsample are also provided which comprise a container containing at leastone BS249 specific polynucleotide selected from the group consisting ofSEQUENCE ID NOS 1-11, and fragments or complements thereof. These testkits further comprise containers with tools useful for collecting testsamples (such as, for example, blood, urine, saliva and stool). Suchtools include lancets and absorbent paper or cloth for collecting andstabilizing blood; swabs for collecting and stabilizing saliva; and cupsfor collecting and stabilizing urine or stool samples. Collectionmaterials, such as papers, cloths, swabs, cups, and the like, mayoptionally be treated to avoid denaturation or irreversible adsorptionof the sample. The collection materials also may be treated with orcontain preservatives, stabilizers or antimicrobial agents to helpmaintain the integrity of the specimens.

The present invention also provides a purified polynucleotide orfragment thereof derived from a BS249 gene. The purified polynucleotideis capable of selectively hybridizing to the nucleic acid of the BS249gene, or a complement thereof. The polynucleotide has at least 50%identity with a polynucleotide selected from the group consisting ofSEQUENCE ID NOS 1-11, and fragments or complements thereof. Further, thepurified polynucleotide can be produced by recombinant and/or synthetictechniques. The purified recombinant polynucleotide can be containedwithin a recombinant vector. The invention further comprises a host celltransfected with the recombinant vector.

The present invention further provides a recombinant expression systemcomprising a nucleic acid sequence that includes an open reading framederived from BS249. The nucleic acid sequence has at least 50% identitywith a sequence selected from the group consisting of SEQUENCE ID NOS1-11, and fragments or complements thereof. The nucleic acid sequence isoperably linked to a control sequence compatible with a desired host.Also provided is a cell transfected with this recombinant expressionsystem.

The present invention also provides a polypeptide encoded by BS249. Thepolypeptide can be produced by recombinant technology, provided inpurified form, or produced by synthetic techniques. The polypeptidecomprises an amino acid sequence which has at least 50% identity with anamino acid sequence selected from the group consisting of SEQUENCE ID NO23, SEQUENCE ID NO 24, SEQUENCE ID NO 25, SEQUENCE ID NO 26, SEQUENCE IDNO 27, and fragments thereof.

Also provided is a specific binding molecule, such as an antibody, whichspecifically binds to at least one BS249 epitope. The antibody can be apolyclonal or monoclonal antibody. The epitope is derived from an aminoacid sequence selected from the group consisting of SEQUENCE ID NO 23,SEQUENCE ID NO 24, SEQUENCE ID NO 25, SEQUENCE ID NO 26, SEQUENCE ID NO27, and fragments thereof. Assay kits for determining the presence ofBS249 antigen or anti-BS249 antibody in a test sample are also included.In one embodiment, the assay kits comprise a container containing atleast one BS249 polypeptide having at least 50% identity with an aminoacid sequence selected from the group consisting of SEQUENCE ID NO 23,SEQUENCE ID NO 24, SEQUENCE ID NO 25, SEQUENCE ID NO 26, SEQUENCE ID NO27, and fragments thereof. Further, the test kit can comprise acontainer with tools useful for collecting test samples (such as blood,urine, saliva, and stool). Such tools include lancets and absorbentpaper or cloth for collecting and stabilizing blood; swabs forcollecting and stabilizing saliva; and cups for collecting andstabilizing urine or stool samples. Collection materials such as papers,cloths, swabs, cups, and the like, may optionally be treated to avoiddenaturation or irreversible adsorption of the sample. These collectionmaterials also may be treated with or contain preservatives, stabilizersor antimicrobial agents to help maintain the integrity of the specimens.Also, the polypeptide can be attached to a solid phase.

In another embodiment of the invention, antibodies or fragments thereofagainst the BS249 antigen can be used to detect or image localization ofthe antigen in a patient for the purpose of detecting or diagnosing adisease or condition. Such antibodies can be polyclonal or monoclonal,or made by molecular biology techniques, and can be labeled with avariety of detectable labels, including but not limited to radioisotopesand paramagnetic metals. Furthermore, antibodies or fragments thereof,whether monoclonal, polyclonal, or made by molecular biology techniques,can be used as therapeutic agents for the treatment of diseasescharacterized by expression of the BS249 antigen. In the case oftherapeutic applications, the antibody may be used withoutderivitization, or it may be derivitized with a cytotoxic agent such asa radioisotope, enzyme, toxin, drug, prodrug, or the like.

Another assay kit for determining the presence of BS249 antigen oranti-BS249 antibody in a test sample comprises a container containing aspecific binding molecule, such as an antibody, which specifically bindsto a BS249 antigen, wherein the BS249 antigen comprises at least oneBS249-encoded epitope. The BS249 antigen has at least about 50% sequenceidentity to a sequence of a BS249-encoded antigen selected from thegroup consisting of SEQUENCE ID NO 23, SEQUENCE ID NO 24, SEQUENCE ID NO25, SEQUENCE ID NO 26, SEQUENCE ID NO 27, and fragments thereof. Thesetest kits can further comprise containers with tools useful forcollecting test samples (such as blood, urine, saliva, and stool). Suchtools include lancets and absorbent paper or cloth for collecting andstabilizing blood; swabs for collecting and stabilizing saliva; cups forcollecting and stabilizing urine or stool samples. Collection materials,such as papers, cloths, swabs, cups and the like, may optionally betreated to avoid denaturation or irreversible adsorption of the sample.These collection materials also may be treated with, or contain,preservatives, stabilizers or antimicrobial agents to help maintain theintegrity of the specimens. The antibody can be attached to a solidphase.

A method for producing a polypeptide which contains at least one epitopeof BS249 is provided, which method comprises incubating host cellstransfected with an expression vector. This vector comprises apolynucleotide sequence encoding a polypeptide, wherein the polypeptidecomprises an amino acid sequence having at least 50% identity with aBS249 amino acid sequence selected from the group consisting of SEQUENCEID NO 23, SEQUENCE ID NO 24, SEQUENCE ID NO 25, SEQUENCE ID NO 26,SEQUENCE ID NO 27, and fragments thereof.

A method for detecting BS249 antigen in a test sample suspected ofcontaining BS249 antigen also is provided. The method comprisescontacting the test sample with an antibody or fragment thereof whichspecifically binds to at least one epitope of BS249 antigen, for a timeand under conditions sufficient for the formation of antibody/antigencomplexes; and detecting the presence of such complexes containing theantibody as an indication of the presence of BS249 antigen in the testsample. The antibody can be attached to a solid phase and may be eithera monoclonal or polyclonal antibody. Furthermore, the antibodyspecifically binds to at least one BS249 antigen selected from the groupconsisting of SEQUENCE ID NO 23, SEQUENCE ID NO 24, SEQUENCE ID NO 25,SEQUENCE ID NO 26, SEQUENCE ID NO 27, and fragments thereof.

Another method is provided which detects antibodies which specificallybind to BS249 antigen in a test sample suspected of containing theseantibodies. The method comprises contacting the test sample with apolypeptide which contains at least one BS249 epitope, wherein the BS249epitope comprises an amino acid sequence having at least 50% identitywith an amino acid sequence encoded by a BS249 polynucleotide, or afragment thereof. Contacting is performed for a time and underconditions sufficient to allow antigen/antibody complexes to form. Themethod further entails detecting complexes which contain thepolypeptide. The polypeptide can be attached to a solid phase. Further,the polypeptide can be a recombinant protein or a synthetic peptidehaving at least 50% identity with an amino acid sequence selected fromthe group consisting of SEQUENCE ID NO 23, SEQUENCE ID NO 24, SEQUENCEID NO 25, SEQUENCE ID NO 26, SEQUENCE ID NO 27, and fragments thereof.

The present invention provides a cell transfected with a BS249 nucleicacid sequence that encodes at least one epitope of a BS249 antigen, orfragment thereof. The nucleic acid sequence is selected from the groupconsisting of SEQUENCE ID NOS 1-11, and fragments or complementsthereof.

A method for producing antibodies to BS249 antigen also is provided,which method comprises administering to an individual an isolatedimmunogenic polypeptide or fragment thereof, wherein the isolatedimmunogenic polypeptide comprises at least one BS249 epitope. Theimmunogenic polypeptide is administered in an amount sufficient toproduce an immune response. The isolated, immunogenic polypeptidecomprises an amino acid sequence selected from the group consisting ofSEQUENCE ID NO 23, SEQUENCE ID NO 24, SEQUENCE ID NO 25, SEQUENCE ID NO26, SEQUENCE ID NO 27, and fragments thereof.

Another method for producing antibodies which specifically bind to BS249antigen is disclosed, which method comprises administering to anindividual a plasmid comprising a nucleic acid sequence which encodes atleast one BS249 epitope derived from an amino acid sequence selectedfrom the group consisting of SEQUENCE ID NO 23, SEQUENCE ID NO 24,SEQUENCE ID NO 25, SEQUENCE ID NO 26, SEQUENCE ID NO 27, and fragmentsthereof. The plasmid is administered in an amount such that the plasmidis taken up by cells in the individual and expressed at levelssufficient to produce an immune response.

Also provided is a composition of matter that comprises a BS249polynucleotide of at least about 10-12 nucleotides having at least 50%identity with a polynucleotide selected from the group consisting ofSEQUENCE ID NOS 1-11, and fragments or complements thereof. The BS249polynucleotide encodes an amino acid sequence having at least one BS249epitope. Another composition of matter provided by the present inventioncomprises a polypeptide with at least one BS249 epitope of about 8-10amino acids. The polypeptide comprises an amino acid sequence having atleast 50% identity with an amino acid sequence selected from the groupconsisting of SEQUENCE ID NO 23, SEQUENCE ID NO 24, SEQUENCE ID NO 25,SEQUENCE ID NO 26, SEQUENCE ID NO 27, and fragments thereof. Alsoprovided is a gene, or fragment thereof, coding for a BS249 polypeptidewhich has at least 50% identity with SEQUENCE ID NO 23, and a gene, or afragment thereof comprising DNA having at least 50% identity withSEQUENCE ID NO 10 or SEQUENCE ID NO 11.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1D show the nucleotide alignment of clones 3769673 (SEQUENCE IDNO 1), 2479915 (SEQUENCE ID NO 2), 2484355 (SEQUENCE ID NO 3), 2823476(SEQUENCE ID NO 4), 3618587 (SEQUENCE ID NO 5), 2477279 (SEQUENCE ID NO6), 640781 (SEQUENCE ID NO 7), 2476961 (SEQUENCE ID NO 8), 3040836(SEQUENCE ID NO 9), the full-length sequence of clone 3769673[designated as 3769673inh (SEQUENCE ID NO 10)], and the consensussequence (SEQUENCE ID NO 11) derived therefrom.

FIG. 2 shows the contig map depicting the formation of the consensusnucleotide sequence (SEQUENCE ID NO 11) from the nucleotide alignment ofoverlapping clones 3769673 (SEQUENCE ID NO 1), 2479915 (SEQUENCE ID NO2), 2484355 (SEQUENCE ID NO 3), 2823476 (SEQUENCE ID NO 4), 3618587(SEQUENCE ID NO 5), 2477279 (SEQUENCE ID NO 6), 640781 (SEQUENCE ID NO7), 2476961 (SEQUENCE ID NO 8), 3040836 (SEQUENCE ID NO 9), 3769673inh(SEQUENCE ID NO 10).

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides a gene, or a fragment thereof, whichcodes for a BS249 polypeptide having at least about 50% identity withSEQUENCE ID NO 23. The present invention further encompasses a BS249gene, or a fragment thereof, comprising DNA which has at least about 50%identity with SEQUENCE ID NO 10 or SEQUENCE ID NO 11.

The present invention also provides methods for assaying a test samplefor products of a breast tissue gene designated as BS249, whichcomprises making cDNA from mRNA in the test sample, and detecting thecDNA as an indication of the presence of breast tissue gene BS249. Themethod may include an amplification step, wherein one or more portionsof the mRNA from BS249 corresponding to the gene or fragments thereof,is amplified. Methods also are provided for assaying for the translationproducts of BS249. Test samples which may be assayed by the methodsprovided herein include tissues, cells, body fluids and secretions. Thepresent invention also provides reagents such as oligonucleotide primersand polypeptides which are useful in performing these methods.

Portions of the nucleic acid sequences disclosed herein are useful asprimers for the reverse transcription of RNA or for the amplification ofcDNA; or as probes to determine the presence of certain MRNA sequencesin test samples. Also disclosed are nucleic acid sequences which permitthe production of encoded polypeptide sequences which are useful asstandards or reagents in diagnostic immunoassays, as targets forpharmaceutical screening assays and/or as components or as target sitesfor various therapies. Monoclonal and polyclonal antibodies directedagainst at least one epitope contained within these polypeptidesequences are useful as delivery agents for therapeutic agents as wellas for diagnostic tests and for screening for diseases or conditionsassociated with BS249, especially breast cancer. Isolation of sequencesof other portions of the gene of interest can be accomplished utilizingprobes or PCR primers derived from these nucleic acid sequences. Thisallows additional probes of the mRNA or cDNA of interest to beestablished, as well as corresponding encoded polypeptide sequences.These additional molecules are useful in detecting, diagnosing, staging,monitoring, prognosticating, in vivo imaging, preventing or treating, ordetermining the predisposition to diseases and conditions of the breast,such as breast cancer, characterized by BS249, as disclosed herein.

The compositions and methods described herein will enable theidentification of certain markers as indicative of a breast tissuedisease or condition; the information obtained therefrom will aid in thedetecting, diagnosing, staging, monitoring, prognosticating, in vivoimaging, preventing or treating, or determining diseases or conditionsassociated with BS249, especially breast cancer. Test methods include,for example, probe assays which utilize the sequence(s) provided hereinand which also may utilize nucleic acid amplification methods such asthe polymerase chain reaction (PCR), the ligase chain reaction (LCR),and hybridization.

In addition, the nucleotide sequences provided herein contain openreading frames from which an immunogenic epitope may be found. Thisepitope is believed to be unique to the disease state or conditionassociated with BS249. It also is thought that the polynucleotides orpolypeptides and protein encoded by the BS249 gene are useful as amarker. This marker is either elevated in disease such as breast cancer,altered in disease such as breast cancer, or present as a normal proteinbut appearing in an inappropriate body compartment. The uniqueness ofthe epitope may be determined by (i) its immunological reactivity andspecificity with antibodies directed against proteins and polypeptidesencoded by the BS249 gene, and (ii) its nonreactivity with any othertissue markers. Methods for determining immunological reactivity arewell-known and include, but are not limited to, for example,radioimmunoassay (RIA), enzyme-linked immunoabsorbent assay (ELISA),hemagglutination (HA), fluorescence polarization immunoassay (FPIA),chemiluminescent immunoassay (CLIA) and others. Several examples ofsuitable methods are described herein.

Unless otherwise stated, the following terms shall have the followingmeanings:

A polynucleotide “derived from” or “specific for” a designated sequencerefers to a polynucleotide sequence which comprises a contiguoussequence of approximately at least about 6 nucleotides, preferably atleast about 8 nucleotides, more preferably at least about 10-12nucleotides, and even more preferably at least about 15-20 nucleotidescorresponding, i.e., identical or complementary to, a region of thedesignated nucleotide sequence. The sequence may be complementary oridentical to a sequence which is unique to a particular polynucleotidesequence as determined by techniques known in the art. Comparisons tosequences in databanks, for example, can be used as a method todetermine the uniqueness of a designated sequence. Regions from whichsequences may be derived, include but are not limited to, regionsencoding specific epitopes, as well as non-translated and/ornon-transcribed regions.

The derived polynucleotide will not necessarily be derived physicallyfrom the nucleotide sequence of interest under study, but may begenerated in any manner, including, but not limited to, chemicalsynthesis, replication, reverse transcription or transcription, which isbased on the information provided by the sequence of bases in theregion(s) from which the polynucleotide is derived. As such, it mayrepresent either a sense or an antisense orientation of the originalpolynucleotide. In addition, combinations of regions corresponding tothat of the designated sequence may be modified in ways known in the artto be consistent with the intended use.

A “fragment” of a specified polynucleotide refers to a polynucleotidesequence which comprises a contiguous sequence of approximately at leastabout 6 nucleotides, preferably at least about 8 nucleotides, morepreferably at least about 10-12 nucleotides, and even more preferably atleast about 15-20 nucleotides corresponding, i.e., identical orcomplementary to, a region of the specified nucleotide sequence.

The term “primer” denotes a specific oligonucleotide sequence which iscomplementary to a target nucleotide sequence and used to hybridize tothe target nucleotide sequence. A primer serves as an initiation pointfor nucleotide polymerization catalyzed by either DNA polymerase, RNApolymerase or reverse transcriptase.

The term “probe” denotes a defined nucleic acid segment (or nucleotideanalog segment, e.g., PNA as defined hereinbelow) which can be used toidentify a specific polynucleotide present in samples bearing thecomplementary sequence.

“Encoded by” refers to a nucleic acid sequence which codes for apolypeptide sequence, wherein the polypeptide sequence or a portionthereof contains an amino acid sequence of at least 3 to 5 amino acids,more preferably at least 8 to 10 amino acids, and even more preferablyat least 15 to 20 amino acids from a polypeptide encoded by the nucleicacid sequence. Also encompassed are polypeptide sequences which areimmunologically identifiable with a polypeptide encoded by the sequence.Thus, a “polypeptide,” “protein,” or “amino acid” sequence has at leastabout 50% identity, preferably about 60% identity, more preferably about75-85% identity, and most preferably about 90-95% or more identity witha BS249 amino acid sequence. Further, the BS249 “polypeptide,”“protein,” or “amino acid” sequence may have at least about 60%similarity, preferably at least about 75% similarity, more preferablyabout 85% similarity, and most preferably about 95% or more similarityto a polypeptide or amino acid sequence of BS249. This amino acidsequence can be selected from the group consisting of SEQUENCE ID NO 23,SEQUENCE ID NO 24, SEQUENCE ID NO 25, SEQUENCE ID NO 26, SEQUENCE ID NO27, and fragments thereof.

A “recombinant polypeptide,” “recombinant protein,” or “a polypeptideproduced by recombinant techniques,” which terms may be usedinterchangeably herein, describes a polypeptide which by virtue of itsorigin or manipulation is not associated with all or a portion of thepolypeptide with which it is associated in nature and/or is linked to apolypeptide other than that to which it is linked in nature. Arecombinant or encoded polypeptide or protein is not necessarilytranslated from a designated nucleic acid sequence. It also may begenerated in any manner, including chemical synthesis or expression of arecombinant expression system.

The term “synthetic peptide” as used herein means a polymeric form ofamino acids of any length, which may be chemically synthesized bymethods well-known to the routineer. These synthetic peptides are usefulin various applications.

The term “polynucleotide” as used herein means a polymeric form ofnucleotides of any length, either ribonucleotides ordeoxyribonucleotides. This term refers only to the primary structure ofthe molecule. Thus, the term includes double- and single-stranded DNA,as well as double- and single-stranded RNA. It also includesmodifications, such as methylation or capping and unmodified forms ofthe polynucleotide. The terms “polynucleotide,” “oligomer,”“oligonucleotide,” and “oligo” are used interchangeably herein.

“A sequence corresponding to a cDNA” means that the sequence contains apolynucleotide sequence that is identical or complementary to a sequencein the designated DNA. The degree (or “percent”) of identity orcomplementarity to the cDNA will be approximately 50% or greater,preferably at least about 70% or greater, and more preferably at leastabout 90% or greater. The sequence that corresponds to the identifiedcDNA will be at least about 50 nucleotides in length, preferably atleast about 60 nucleotides in length, and more preferably at least about70 nucleotides in length. The correspondence between the gene or genefragment of interest and the cDNA can be determined by methods known inthe art and include, for example, a direct comparison of the sequencedmaterial with the cDNAs described, or hybridization and digestion withsingle strand nucleases, followed by size determination of the digestedfragments.

Techniques for determining amino acid sequence “similarity” arewell-known in the art. In general, “similarity” means the exact aminoacid to amino acid comparison of two or more polypeptides at theappropriate place, where amino acids are identical or possess similarchemical and/or physical properties such as charge or hydrophobicity. Aso-termed “percent similarity” then can be determined between thecompared polypeptide sequences. Techniques for determining nucleic acidand amino acid sequence identity also are well known in the art andinclude determining the nucleotide sequence of the mRNA for that gene(usually via a cDNA intermediate) and determining the amino acidsequence encoded thereby, and comparing this to a second amino acidsequence. In general, “identity” refers to an exact nucleotide tonucleotide or amino acid to amino acid correspondence of twopolynucleotides or polypeptide sequences, respectively. Two or morepolynucleotide sequences can be compared by determining their “percentidentity.” Two or more amino acid sequences likewise can be compared bydetermining their “percent identity.” The percent identity of twosequences, whether nucleic acid or peptide sequences, is the number ofexact matches between two aligned sequences divided by the length of theshorter sequences and multiplied by 100. An approximate alignment fornucleic acid sequences is provided by the local homology algorithm ofSmith and Waterman, Advances in Applied Mathematics 2:482-489 (1981).This algorithm can be extended to use with peptide sequences using thescoring matrix developed by Dayhoff, Atlas of Protein Sequences andStructure, M. O. Dayhoff ed., 5 suppl. 3:353-358, National BiomedicalResearch Foundation, Washington, D.C., USA, and normalized by Gribskov,Nucl. Acids Res. 14(6):6745-6763 (1986). An implementation of thisalgorithm for nucleic acid and peptide sequences is provided by theGenetics Computer Group (Madison, Wis.) in their BestFit utilityapplication. The default parameters for this method are described in theWisconsin Sequence Analysis Package Program Manual, Version 8 (1995)(available from Genetics Computer Group, Madison, Wis.). Other equallysuitable programs for calculating the percent identity or similaritybetween sequences are generally known in the art.

“Purified polynucleotide” refers to a polynucleotide of interest orfragment thereof which is essentially free, e.g., contains less thanabout 50%, preferably less than about 70%, and more preferably less thanabout 90%, of the protein with which the polynucleotide is naturallyassociated. Techniques for purifying polynucleotides of interest arewell-known in the art and include, for example, disruption of the cellcontaining the polynucleotide with a chaotropic agent and separation ofthe polynucleotide(s) and proteins by ion-exchange chromatography,affinity chromatography and sedimentation according to density.

“Purified polypeptide” or “purified protein” means a polypeptide ofinterest or fragment thereof which is essentially free of, e.g.,contains less than about 50%, preferably less than about 70%, and morepreferably less than about 90%, cellular components with which thepolypeptide of interest is naturally associated. Methods for purifyingpolypeptides of interest are known in the art.

The term “isolated” means that the material is removed from its originalenvironment (e.g., the natural environment if it is naturallyoccurring). For example, a naturally-occurring polynucleotide orpolypeptide present in a living animal is not isolated, but the samepolynucleotide or DNA or polypeptide, which is separated from some orall of the coexisting materials in the natural system, is isolated. Suchpolynucleotide could be part of a vector and/or such polynucleotide orpolypeptide could be part of a composition, and still be isolated inthat the vector or composition is not part of its natural environment.

“Polypeptide” and “protein” are used interchangeably herein and indicateat least one molecular chain of amino acids linked through covalentand/or non-covalent bonds. The terms do not refer to a specific lengthof the product. Thus peptides, oligopeptides and proteins are includedwithin the definition of polypeptide. The terms includepost-translational modifications of the polypeptide, for example,glycosylations, acetylations, phosphorylations and the like. Inaddition, protein fragments, analogs, mutated or variant proteins,fusion proteins and the like are included within the meaning ofpolypeptide.

A “fragment” of a specified polypeptide refers to an amino acid sequencewhich comprises at least about 3-5 amino acids, more preferably at leastabout 8-10 amino acids, and even more preferably at least about 15-20amino acids derived from the specified polypeptide.

“Recombinant host cells,” “host cells,” “cells,” “cell lines,” “cellcultures,” and other such terms denoting microorganisms or highereukaryotic cell lines cultured as unicellular entities refer to cellswhich can be, or have been, used as recipients for recombinant vector orother transferred DNA, and include the original progeny of the originalcell which has been transfected.

As used herein “replicon” means any genetic element, such as a plasmid,a chromosome or a virus, that behaves as an autonomous unit ofpolynucleotide replication within a cell.

A “vector” is a replicon in which another polynucleotide segment isattached, such as to bring about the replication and/or expression ofthe attached segment.

The term “control sequence” refers to a polynucleotide sequence which isnecessary to effect the expression of a coding sequence to which it isligated. The nature of such control sequences differs depending upon thehost organism. In prokaryotes, such control sequences generally includea promoter, a ribosomal binding site and terminators; in eukaryotes,such control sequences generally include promoters, terminators and, insome instances, enhancers. The term “control sequence” thus is intendedto include at a minimum all components whose presence is necessary forexpression, and also may include additional components whose presence isadvantageous, for example, leader sequences.

“Operably linked” refers to a situation wherein the components describedare in a relationship permitting them to function in their intendedmanner. Thus, for example, a control sequence “operably linked” to acoding sequence is ligated in such a manner that expression of thecoding sequence is achieved under conditions compatible with the controlsequence.

The term “open reading frame” or “ORF” refers to a region of apolynucleotide sequence which encodes a polypeptide. This region mayrepresent a portion of a coding sequence or a total coding sequence.

A “coding sequence” is a polynucleotide sequence which is transcribedinto mRNA and translated into a polypeptide when placed under thecontrol of appropriate regulatory sequences. The boundaries of thecoding sequence are determined by a translation start codon at the5′-terminus and a translation stop codon at the 3′-terminus. A codingsequence can include, but is not limited to, mRNA, cDNA and recombinantpolynucleotide sequences.

The term “immunologically identifiable with/as” refers to the presenceof epitope(s) and polypeptide(s) which also are present in and areunique to the designated polypeptide(s). Immunological identity may bedetermined by antibody binding and/or competition in binding. Thesetechniques are known to the routineer and also are described herein. Theuniqueness of an epitope also can be determined by computer searches ofknown data banks, such as GenBank, for the polynucleotide sequence whichencodes the epitope and by amino acid sequence comparisons with otherknown proteins.

As used herein, “epitope” means an antigenic determinant of apolypeptide or protein. Conceivably, an epitope can comprise three aminoacids in a spatial conformation which is unique to the epitope.Generally, an epitope consists of at least five such amino acids andmore usually, it consists of at least eight to ten amino acids. Methodsof examining spatial conformation are known in the art and include, forexample, x-ray crystallography and two-dimensional nuclear magneticresonance.

A “conformational epitope” is an epitope that is comprised of a specificjuxtaposition of amino acids in an immunologically recognizablestructure, such amino acids being present on the same polypeptide in acontiguous or non-contiguous order or present on different polypeptides.

A polypeptide is “immunologically reactive” with an antibody when itbinds to an antibody due to antibody recognition of a specific epitopecontained within the polypeptide. Immunological reactivity may bedetermined by antibody binding, more particularly, by the kinetics ofantibody binding, and/or by competition in binding using ascompetitor(s) a known polypeptide(s) containing an epitope against whichthe antibody is directed. The methods for determining whether apolypeptide is immunologically reactive with an antibody are known inthe art.

As used herein, the term “immunogenic polypeptide containing an epitopeof interest” means naturally occurring polypeptides of interest orfragments thereof, as well as polypeptides prepared by other means, forexample, by chemical synthesis or the expression of the polypeptide in arecombinant organism.

The term “transfection” refers to the introduction of an exogenouspolynucleotide into a prokaryotic or eucaryotic host cell, irrespectiveof the method used for the introduction. The term “transfection” refersto both stable and transient introduction of the polynucleotide, andencompasses direct uptake of polynucleotides, transformation,transduction, and f-mating. Once introduced into the host cell, theexogenous polynucleotide may be maintained as a non-integrated replicon,for example, a plasmid, or alternatively, may be integrated into thehost genome.

“Treatment” refers to prophylaxis and/or therapy.

The term “individual” as used herein refers to vertebrates, particularlymembers of the mammalian species and includes, but is not limited to,domestic animals, sports animals, primates and humans; moreparticularly, the term refers to humans.

The term “sense strand” or “plus strand” (or “+”) as used herein denotesa nucleic acid that contains the sequence that encodes the polypeptide.The term “antisense strand” or “minus strand” (or “−”) denotes a nucleicacid that contains a sequence that is complementary to that of the“plus” strand.

The term “test sample” refers to a component of an individual's bodywhich is the source of the analyte (such as antibodies of interest orantigens of interest). These components are well known in the art. Atest sample is typically anything suspected of containing a targetsequence. Test samples can be prepared using methodologies well known inthe art such as by obtaining a specimen from an individual and, ifnecessary, disrupting any cells contained thereby to release targetnucleic acids. These test samples include biological samples which canbe tested by the methods of the present invention described herein andinclude human and animal body fluids such as whole blood, serum, plasma,cerebrospinal fluid, sputum, bronchial washing, bronchial aspirates,urine, lymph fluids, and various external secretions of the respiratory,intestinal and genitourinary tracts, tears, saliva, milk, white bloodcells, myelomas and the like; biological fluids such as cell culturesupernatants; tissue specimens which may be fixed; and cell specimenswhich may be fixed.

“Purified product” refers to a preparation of the product which has beenisolated from the cellular constituents with which the product isnormally associated and from other types of cells which may be presentin the sample of interest.

“PNA” denotes a “peptide nucleic acid analog” which may be utilized in aprocedure such as an assay described herein to determine the presence ofa target. “MA” denotes a “morpholino analog” which may be utilized in aprocedure such as an assay described herein to determine the presence ofa target. See, for example, U.S. Pat. No. 5,378,841, which isincorporated herein by reference. PNAs are neutrally charged moietieswhich can be directed against RNA targets or DNA. PNA probes used inassays in place of, for example, the DNA probes of the presentinvention, offer advantages not achievable when DNA probes are used.These advantages include manufacturability, large scale labeling,reproducibility, stability, insensitivity to changes in ionic strengthand resistance to enzymatic degradation which is present in methodsutilizing DNA or RNA. These PNAs can be labeled with (“attached to”)such signal generating compounds as fluorescein, radionucleotides,chemiluminescent compounds and the like. PNAs or other nucleic acidanalogs such as MAs thus can be used in assay methods in place of DNA orRNA. Although assays are described herein utilizing DNA probes, it iswithin the scope of the routineer that PNAs or MAs can be substitutedfor RNA or DNA with appropriate changes if and as needed in assayreagents.

“Analyte,” as used herein, is the substance to be detected which may bepresent in the test sample. The analyte can be any substance for whichthere exists a naturally occurring specific binding member (such as anantibody), or for which a specific binding member can be prepared. Thus,an analyte is a substance that can bind to one or more specific bindingmembers in an assay. “Analyte” also includes any antigenic substances,haptens, antibodies and combinations thereof. As a member of a specificbinding pair, the analyte can be detected by means of naturallyoccurring specific binding partners (pairs) such as the use of intrinsicfactor protein as a member of a specific binding pair for thedetermination of Vitamin B12, the use of folate-binding protein todetermine folic acid, or the use of a lectin as a member of a specificbinding pair for the determination of a carbohydrate. The analyte caninclude a protein, a polypeptide, an amino acid, a nucleotide target andthe like. The analyte can be soluble in a body fluid such as blood,blood plasma or serum, urine or the like. The analyte can be in atissue, either on a cell surface or within a cell. The analyte can be onor in a cell dispersed in a body fluid such as blood, urine, breastaspirate, or obtained as a biopsy sample.

The terms “diseases of the breast,” “breast disease,” and “condition ofthe breast” are used interchangeably herein to refer to any disease orcondition of the breast including, but not limited to, atypicalhyperplasia, fibroadenoma, cystic breast disease, and cancer.

“Breast cancer,” as used herein, refers to any malignant disease of thebreast including, but not limited to, ductal carcinoma in situ, lobularcarcinoma in situ, infiltrating ductal carcinoma, medullary carcinoma,tubular carcinoma, mucinous carcinoma, infiltrating lobular carcinoma,infiltrating comedocarcinoma and inflammatory carcinoma.

An “Expressed Sequence Tag” or “EST” refers to the partial sequence of acDNA insert which has been made by reverse transcription of mRNAextracted from a tissue followed by insertion into a vector.

A “transcript image” refers to a table or list giving the quantitativedistribution of ESTs in a library and represents the genes active in thetissue from which the library was made.

The present invention provides assays which utilize specific bindingmembers. A “specific binding member,” as used herein, is a member of aspecific binding pair. That is, two different molecules where one of themolecules, through chemical or physical means, specifically binds to thesecond molecule. Therefore, in addition to antigen and antibody specificbinding pairs of common immunoassays, other specific binding pairs caninclude biotin and avidin, carbohydrates and lectins, complementarynucleotide sequences, effector and receptor molecules, cofactors andenzymes, enzyme inhibitors, and enzymes and the like. Furthermore,specific binding pairs can include members that are analogs of theoriginal specific binding members, for example, an analyte-analog.Immunoreactive specific binding members include antigens, antigenfragments, antibodies and antibody fragments, both monoclonal andpolyclonal and complexes thereof, including those formed by recombinantDNA molecules.

Specific binding members include “specific binding molecules.” A“specific binding molecule” intends any specific binding member,particularly an immunoreactive specific binding member. As such, theterm “specific binding molecule” encompasses antibody molecules(obtained from both polyclonal and monoclonal preparations), as well as,the following: hybrid (chimeric) antibody molecules (see, for example,Winter, et al., Nature 349:293-299 (1991), and U.S. Pat. No. 4,816,567);F(ab′)₂ and F(ab) fragments; Fv molecules (non-covalent heterodimers,see, for example, Inbar, et al., Proc. Natl. Acad. Sci. USA 69:2659-2662(1972), and Ehrlich, et al., Biochem. 19:4091-4096 (1980)); single chainFv molecules (sFv) (see, for example, Huston, et al., Proc. Natl. Acad.Sci. USA 85:5879-5883 (1988)); humanized antibody molecules (see, forexample, Riechmann, et al., Nature 332:323-327 (1988), Verhoeyan, etal., Science 239:1534-1536 (1988), and UK Patent Publication No. GB2,276,169, published Sep. 21, 1994); and, any functional fragmentsobtained from such molecules, wherein such fragments retainimmunological binding properties of the parent antibody molecule.

The term “hapten,” as used herein, refers to a partial antigen ornon-protein binding member which is capable of binding to an antibody,but which is not capable of eliciting antibody formation unless coupledto a carrier protein.

A “capture reagent,” as used herein, refers to an unlabeled specificbinding member which is specific either for the analyte as in a sandwichassay, for the indicator reagent or analyte as in a competitive assay,or for an ancillary specific binding member, which itself is specificfor the analyte, as in an indirect assay. The capture reagent can bedirectly or indirectly bound to a solid phase material before theperformance of the assay or during the performance of the assay, therebyenabling the separation of immobilized complexes from the test sample.

The “indicator reagent” comprises a “signal-generating compound”(“label”) which is capable of generating and generates a measurablesignal detectable by external means, conjugated (“attached”) to aspecific binding member. In addition to being an antibody member of aspecific binding pair, the indicator reagent also can be a member of anyspecific binding pair, including either hapten-anti-hapten systems suchas biotin or anti-biotin, avidin or biotin, a carbohydrate or a lectin,a complementary nucleotide sequence, an effector or a receptor molecule,an enzyme cofactor and an enzyme, an enzyme inhibitor or an enzyme andthe like. An immunoreactive specific binding member can be an antibody,an antigen, or an antibody/antigen complex that is capable of bindingeither to the polypeptide of interest as in a sandwich assay, to thecapture reagent as in a competitive assay, or to the ancillary specificbinding member as in an indirect assay. When describing probes and probeassays, the term “reporter molecule” may be used. A reporter moleculecomprises a signal generating compound as described hereinaboveconjugated to a specific binding member of a specific binding pair, suchas carbazole or adamantane.

The various “signal-generating compounds” (labels) contemplated includechromagens, catalysts such as enzymes, luminescent compounds such asfluorescein and rhodamine, chemiluminescent compounds such asdioxetanes, acridiniums, phenanthridiniums and luminol, radioactiveelements and direct visual labels. Examples of enzymes include alkalinephosphatase, horseradish peroxidase, beta-galactosidase and the like.The selection of a particular label is not critical, but it must becapable of producing a signal either by itself or in conjunction withone or more additional substances.

“Solid phases” (“solid supports”) are known to those in the art andinclude the walls of wells of a reaction tray, test tubes, polystyrenebeads, magnetic or non-magnetic beads, nitrocellulose strips, membranes,microparticles such as latex particles, sheep (or other animal) redblood cells and Duracytes® (red blood cells “fixed” by pyruvic aldehydeand formaldehyde, available from Abbott Laboratories, Abbott Park, Ill.)and others. The “solid phase” is not critical and can be selected by oneskilled in the art. Thus, latex particles, microparticles, magnetic ornon-magnetic beads, membranes, plastic tubes, walls of microtiter wells,glass or silicon chips, sheep (or other suitable animal's) red bloodcells and Duracytes® are all suitable examples. Suitable methods forimmobilizing peptides on solid phases include ionic, hydrophobic,covalent interactions and the like. A “solid phase,” as used herein,refers to any material which is insoluble, or can be made insoluble by asubsequent reaction. The solid phase can be chosen for its intrinsicability to attract and immobilize the capture reagent. Alternatively,the solid phase can retain an additional receptor which has the abilityto attract and immobilize the capture reagent. The additional receptorcan include a charged substance that is oppositely charged with respectto the capture reagent itself or to a charged substance conjugated tothe capture reagent. As yet another alternative, the receptor moleculecan be any specific binding member which is immobilized upon (attachedto) the solid phase and which has the ability to immobilize the capturereagent through a specific binding reaction. The receptor moleculeenables the indirect binding of the capture reagent to a solid phasematerial before the performance of the assay or during the performanceof the assay. The solid phase thus can be a plastic, derivatizedplastic, magnetic or non-magnetic metal, glass or silicon surface of atest tube, microtiter well, sheet, bead, microparticle, chip, sheep (orother suitable animal's) red blood cells, Duracytes® and otherconfigurations known to those of ordinary skill in the art.

It is contemplated and within the scope of the present invention thatthe solid phase also can comprise any suitable porous material withsufficient porosity to allow access by detection antibodies and asuitable surface affinity to bind antigens. Microporous structuresgenerally are preferred, but materials with a gel structure in thehydrated state may be used as well. Such useful solid supports include,but are not limited to, nitrocellulose and nylon. It is contemplatedthat such porous solid supports described herein preferably are in theform of sheets of thickness from about 0.01 to 0.5 mm, preferably about0.1 mm. The pore size may vary within wide limits and preferably is fromabout 0.025 to 15 microns, especially from about 0.15 to 15 microns. Thesurface of such supports may be activated by chemical processes whichcause covalent linkage of the antigen or antibody to the support. Theirreversible binding of the antigen or antibody is obtained, however, ingeneral, by adsorption on the porous material by poorly understoodhydrophobic forces. Other suitable solid supports are known in the art.

Reagents

The present invention provides reagents such as polynucleotide sequencesderived from a breast tissue of interest and designated as BS249,polypeptides encoded thereby and antibodies specific for thesepolypeptides. The present invention also provides reagents such asoligonucleotide fragments derived from the disclosed polynucleotides andnucleic acid sequences complementary to these polynucleotides. Thepolynucleotides, polypeptides, or antibodies of the present inventionmay be used to provide information leading to the detecting, diagnosing,staging, monitoring, prognosticating, in vivo imaging, preventing ortreating of, or determining the predisposition to, diseases andconditions of the breast, such as breast cancer. The sequences disclosedherein represent unique polynucleotides which can be used in assays orfor producing a specific profile of gene transcription activity. Suchassays are disclosed in European Patent Number 0373203B1 andInternational Publication No. WO 95/11995, which are hereby incorporatedby reference.

Selected BS249-derived polynucleotides can be used in the methodsdescribed herein for the detection of normal or altered gene expression.Such methods may employ BS249 polynucleotides or oligonucleotides,fragments or derivatives thereof, or nucleic acid sequencescomplementary thereto.

The polynucleotides disclosed herein, their complementary sequences, orfragments of either, can be used in assays to detect, amplify orquantify genes, nucleic acids, cDNAs or mRNAs relating to breast tissuedisease and conditions associated therewith. They also can be used toidentify an entire or partial coding region of a BS249 polypeptide. Theyfurther can be provided in individual containers in the form of a kitfor assays, or provided as individual compositions. If provided in a kitfor assays, other suitable reagents such as buffers, conjugates and thelike may be included.

The polynucleotide may be in the form of RNA or DNA. Polynucleotides inthe form of DNA, cDNA, genomic DNA, nucleic acid analogs and syntheticDNA are within the scope of the present invention. The DNA may bedouble-stranded or single-stranded, and if single stranded, may be thecoding (sense) strand or non-coding (anti-sense) strand. The codingsequence which encodes the polypeptide may be identical to the codingsequence provided herein or may be a different coding sequence whichcoding sequence, as a result of the redundancy or degeneracy of thegenetic code, encodes the same polypeptide as the DNA provided herein.

This polynucleotide may include only the coding sequence for thepolypeptide, or the coding sequence for the polypeptide and anadditional coding sequence such as a leader or secretory sequence or aproprotein sequence, or the coding sequence for the polypeptide (andoptionally an additional coding sequence) and non-coding sequence, suchas a non-coding sequence 5′ and/or 3′ of the coding sequence for thepolypeptide.

In addition, the invention includes variant polynucleotides containingmodifications such as polynucleotide deletions, substitutions oradditions; and any polypeptide modification resulting from the variantpolynucleotide sequence. A polynucleotide of the present invention alsomay have a coding sequence which is a naturally occurring allelicvariant of the coding sequence provided herein.

In addition, the coding sequence for the polypeptide may be fused in thesame reading frame to a polynucleotide sequence which aids in expressionand secretion of a polypeptide from a host cell, for example, a leadersequence which functions as a secretory sequence for controllingtransport of a polypeptide from the cell. The polypeptide having aleader sequence is a preprotein and may have the leader sequence cleavedby the host cell to form the polypeptide. The polynucleotides may alsoencode for a proprotein which is the protein plus additional 5′ aminoacid residues. A protein having a prosequence is a proprotein and may,in some cases, be an inactive form of the protein. Once the prosequenceis cleaved, an active protein remains. Thus, the polynucleotide of thepresent invention may encode for a protein, or for a protein having aprosequence, or for a protein having both a presequence (leadersequence) and a prosequence.

The polynucleotides of the present invention may also have the codingsequence fused in frame to a marker sequence which allows forpurification of the polypeptide of the present invention. The markersequence may be a hexa-histidine tag supplied by a pQE-9 vector toprovide for purification of the polypeptide fused to the marker in thecase of a bacterial host, or, for example, the marker sequence may be ahemagglutinin (HA) tag when a mammalian host, e.g. a COS-7 cell line, isused. The HA tag corresponds to an epitope derived from the influenzahemagglutinin protein. See, for example, I. Wilson et al., Cell 37:767(1984).

It is contemplated that polynucleotides will be considered to hybridizeto the sequences provided herein if there is at least 50%, preferably atleast 70%, and more preferably at least 90% identity between thepolynucleotide and the sequence.

The degree of sequence identity between two nucleic acid moleculesgreatly affects the efficiency and strength of hybridization eventsbetween such molecules. A partially identical nucleic acid sequence isone that will at least partially inhibit a completely identical sequencefrom hybridizing to a target molecule. Inhibition of hybridization ofthe completely identical sequence can be assessed using hybridizationassays that are well known in the art (e.g., Southern blot, Northernblot, solution hybridization, in situ hybridization, or the like, seeSambrook, et al., Molecular Cloning: A Laboratory Manual, SecondEdition, (1989) Cold Spring Harbor, N.Y.). Such assays can be conductedusing varying degrees of selectivity, for example, using conditionsvarying from low to high stringency. If conditions of low stringency areemployed, the absence of non-specific binding can be assessed using asecondary probe that lacks even a partial degree of sequence identity(for example, a probe having less than about 30% sequence identity withthe target molecule), such that, in the absence of non-specific bindingevents, the secondary probe will not hybridize to the target.

When utilizing a hybridization-based detection system, a nucleic acidprobe is chosen that is complementary to a target nucleic acid sequence,and then by selection of appropriate conditions the probe and the targetsequence “selectively hybridize,” or bind, to each other to form ahybrid molecule. In one embodiment of the present invention, a nucleicacid molecule is capable of hybridizing selectively to a target sequenceunder moderately stringent hybridization conditions. In the context ofthe present invention, moderately stringent hybridization conditionsallow detection of a target nucleic acid sequence of at least 14nucleotides in length having at least approximately 70% sequenceidentity with the sequence of the selected nucleic acid probe. Inanother embodiment, such selective hybridization is performed understringent hybridization conditions. Stringent hybridization conditionsallow detection of target nucleic acid sequences of at least 14nucleotides in length having a sequence identity of greater than 90%with the sequence of the selected nucleic acid probe. Hybridizationconditions useful for probe/target hybridization where the probe andtarget have a specific degree of sequence identity, can be determined asis known in the art (see, for example, Nucleic Acid Hybridization: APractical Approach, editors B. D. Hames and S. J. Higgins, (1985)Oxford; Washington, D.C.; IRL Press). Hybrid molecules can be formed,for example, on a solid support, in solution, and in tissue sections.The formation of hybrids can be monitored by inclusion of a reportermolecule, typically, in the probe. Such reporter molecules, ordetectable elements include, but are not limited to, radioactiveelements, fluorescent markers, and molecules to which anenzyme-conjugated ligand can bind.

With respect to stringency conditions for hybridization, it is wellknown in the art that numerous equivalent conditions can be employed toestablish a particular stringency by varying, for example, the followingfactors: the length and nature of probe and target sequences, basecomposition of the various sequences, concentrations of salts and otherhybridization solution components, the presence or absence of blockingagents in the hybridization solutions (e.g., formamide, dextran sulfate,and polyethylene glycol), hybridization reaction temperature and timeparameters, as well as, varying wash conditions. The selection of aparticular set of hybridization conditions is well within the skill ofthe routineer in the art (see, for example, Sambrook, et al., MolecularCloning: A Laboratory Manual, Second Edition, (1989) Cold Spring Harbor,N.Y.).

The present invention also provides an antibody produced by using apurified BS249 polypeptide of which at least a portion of thepolypeptide is encoded by a BS249 polynucleotide selected from thepolynucleotides provided herein. These antibodies may be used in themethods provided herein for the detection of BS249 antigen in testsamples. The presence of BS249 antigen in the test samples is indicativeof the presence of a breast disease or condition. The antibody also maybe used for therapeutic purposes, for example, in neutralizing theactivity of BS249 polypeptide in conditions associated with altered orabnormal expression.

The present invention further relates to a BS249 polypeptide which hasthe deduced amino acid sequence as provided herein, as well asfragments, analogs and derivatives of such polypeptide. The polypeptideof the present invention may be a recombinant polypeptide, a naturalpurified polypeptide or a synthetic polypeptide. The fragment,derivative or analog of the BS249 polypeptide may be one in which one ormore of the amino acid residues is substituted with a conserved ornon-conserved amino acid residue (preferably a conserved amino acidresidue) and such substituted amino acid residue may or may not be oneencoded by the genetic code; or it may be one in which one or more ofthe amino acid residues includes a substituent group; or it may be onein which the polypeptide is fused with another compound, such as acompound to increase the half-life of the polypeptide (for example,polyethylene glycol); or it may be one in which the additional aminoacids are fused to the polypeptide, such as a leader or secretorysequence or a sequence which is employed for purification of thepolypeptide or a proprotein sequence. Such fragments, derivatives andanalogs are within the scope of the present invention. The polypeptidesand polynucleotides of the present invention are provided preferably inan isolated form and preferably purified.

Thus, a polypeptide of the present invention may have an amino acidsequence that is identical to that of the naturally occurringpolypeptide or that is different by minor variations due to one or moreamino acid substitutions. The variation may be a “conservative change”typically in the range of about 1 to 5 amino acids, wherein thesubstituted amino acid has similar structural or chemical properties,e.g., replacement of leucine with isoleucine or threonine with serine.In contrast, variations may include nonconservative changes, e.g.,replacement of a glycine with a tryptophan. Similar minor variations mayalso include amino acid deletions or insertions, or both. Guidance indetermining which and how many amino acid residues may be substituted,inserted or deleted without changing biological or immunologicalactivity may be found using computer programs well known in the art, forexample, DNASTAR software (DNASTAR Inc., Madison Wis.).

Probes constructed according to the polynucleotide sequences of thepresent invention can be used in various assay methods to providevarious types of analysis. For example, such probes can be used influorescent in situ hybridization (FISH) technology to performchromosomal analysis, and used to identify cancer-specific structuralalterations in the chromosomes, such as deletions or translocations thatare visible from chromosome spreads or detectable using PCR-generatedand/or allele specific oligonucleotides probes, allele specificamplification or by direct sequencing. Probes also can be labeled withradioisotopes, directly- or indirectly-detectable haptens, orfluorescent molecules, and utilized for in situ hybridization studies toevaluate the mRNA expression of the gene comprising the polynucleotidein tissue specimens or cells.

This invention also provides teachings as to the production of thepolynucleotides and polypeptides provided herein.

Probe Assays

The sequences provided herein may be used to produce probes which can beused in assays for the detection of nucleic acids in test samples. Theprobes may be designed from conserved nucleotide regions of thepolynucleotides of interest or from non-conserved nucleotide regions ofthe polynucleotide of interest. The design of such probes foroptimization in assays is within the skill of the routineer. Generally,nucleic acid probes are developed from non-conserved or unique regionswhen maximum specificity is desired, and nucleic acid probes aredeveloped from conserved regions when assaying for nucleotide regionsthat are closely related to, for example, different members of amulti-gene family or in related species like mouse and man.

The polymerase chain reaction (PCR) is a technique for amplifying adesired nucleic acid sequence (target) contained in a nucleic acid ormixture thereof. In PCR, a pair of primers are employed in excess tohybridize to the complementary strands of the target nucleic acid. Theprimers are each extended by a polymerase using the target nucleic acidas a template. The extension products become target sequencesthemselves, following dissociation from the original target strand. Newprimers then are hybridized and extended by a polymerase, and the cycleis repeated to geometrically increase the number of target sequencemolecules. PCR is disclosed in U.S. Pat. Nos. 4,683,195 and 4,683,202,which are incorporated herein by reference.

The Ligase Chain Reaction (LCR) is an alternate method for nucleic acidamplification. In LCR, probe pairs are used which include two primary(first and second) and two secondary (third and fourth) probes, all ofwhich are employed in molar excess to target. The first probe hybridizesto a first segment of the target strand, and the second probe hybridizesto a second segment of the target strand, the first and second segmentsbeing contiguous so that the primary probes abut one another in 5′phosphate-3′ hydroxyl relationship, and so that a ligase can covalentlyfuse or ligate the two probes into a fused product. In addition, a third(secondary) probe can hybridize to a portion of the first probe and afourth (secondary) probe can hybridize to a portion of the second probein a similar abutting fashion. Of course, if the target is initiallydouble stranded, the secondary probes also will hybridize to the targetcomplement in the first instance. Once the ligated strand of primaryprobes is separated from the target strand, it will hybridize with thethird and fourth probes which can be ligated to form a complementary,secondary ligated product. It is important to realize that the ligatedproducts are functionally equivalent to either the target or itscomplement. By repeated cycles of hybridization and ligation,amplification of the target sequence is achieved. This technique isdescribed more completely in EP-A-320 308 to K. Backman published Jun.16, 1989 and EP-A-439 182 to K. Backman et al., published Jul. 31, 1991,both of which are incorporated herein by reference.

For amplification of mRNAs, it is within the scope of the presentinvention to reverse transcribe mRNA into cDNA followed by polymerasechain reaction (RT-PCR); or, to use a single enzyme for both steps asdescribed in U.S. Pat. No. 5,322,770, which is incorporated herein byreference; or reverse transcribe mRNA into cDNA followed by asymmetricgap ligase chain reaction (RT-AGLCR) as described by R. L. Marshall etal., PCR Methods and Applications 4:80-84 (1994), which also isincorporated herein by reference.

Other known amplification methods which can be utilized herein includebut are not limited to the so-called “NASBA” or “3SR” techniquedescribed by J. C. Guatelli et al., Proc. Natl. Acad. Sci. USA87:1874-1878 (1990) and also described by J. Compton, Nature 350 (No.6313):91-92 (1991); Q-beta amplification as described in publishedEuropean Patent Application (EPA) No. 4544610; strand displacementamplification (as described in G. T. Walker et al., Clin. Chem. 42:9-13[1996]) and European Patent Application No. 684315; and target mediatedamplification, as described in International Publication No. WO93/22461.

Detection of BS249 may be accomplished using any suitable detectionmethod, including those detection methods which are currently well knownin the art, as well as detection strategies which may evolve later.Examples of the foregoing presently known detection methods are herebyincorporated herein by reference. See, for example, Caskey et al., U.S.Pat. No. 5,582,989, Gelfand et al., U.S. Pat. No. 5,210,015. Examples ofsuch detection methods include target amplification methods as well assignal amplification technologies. An example of presently knowndetection methods would include the nucleic acid amplificationtechnologies referred to as PCR, LCR, NASBA, SDA, RCR and TMA. See, forexample, Caskey et al., U.S. Pat. No. 5,582,989, Gelfand et al., U.S.Pat. No. 5,210,015. All of the foregoing are hereby incorporated byreference. Detection may also be accomplished using signal amplificationsuch as that disclosed in Snitman et al., U.S. Pat. No. 5,273,882. Whilethe amplification of target or signal is preferred at present, it iscontemplated and within the scope of the present invention thatultrasensitive detection methods which do not require amplification canbe utilized herein.

Detection, both amplified and non-amplified, may be performed using avariety of heterogeneous and homogeneous detection formats. Examples ofheterogeneous detection formats are disclosed in Snitman et al., U.S.Pat. No. 5,273,882, Albarella et al., in EP-84114441.9, Urdea et al.,U.S. Pat. No. 5,124,246, Ullman et al. U.S. Pat. No. 5,185,243 andKourilsky et al., U.S. Pat. No. 4,581,333. All of the foregoing arehereby incorporated by reference. Examples of homogeneous detectionformats are disclosed in, Caskey et al., U.S. Pat. No. 5,582,989,Gelfand et al., U.S. Pat. No. 5,210,015, which are incorporated hereinby reference. Also contemplated and within the scope of the presentinvention is the use of multiple probes in the hybridization assay,which use improves sensitivity and amplification of the BS249 signal.See, for example, Caskey et al., U.S. Pat. No. 5,582,989, Gelfand etal., U.S. Pat. No. 5,210,015, which are incorporated herein byreference.

In one embodiment, the present invention generally comprises the stepsof contacting a test sample suspected of containing a targetpolynucleotide sequence with amplification reaction reagents comprisingan amplification primer, and a detection probe that can hybridize withan internal region of the amplicon sequences. Probes and primersemployed according to the method provided herein are labeled withcapture and detection labels, wherein probes are labeled with one typeof label and primers are labeled with another type of label.Additionally, the primers and probes are selected such that the probesequence has a lower melt temperature than the primer sequences. Theamplification reagents, detection reagents and test sample are placedunder amplification conditions whereby, in the presence of targetsequence, copies of the target sequence (an amplicon) are produced. Inthe usual case, the amplicon is double stranded because primers areprovided to amplify a target sequence and its complementary strand. Thedouble stranded amplicon then is thermally denatured to produce singlestranded amplicon members. Upon formation of the single strandedamplicon members, the mixture is cooled to allow the formation ofcomplexes between the probes and single stranded amplicon members.

As the single stranded amplicon sequences and probe sequences arecooled, the probe sequences preferentially bind the single strandedamplicon members. This finding is counterintuitive given that the probesequences generally are selected to be shorter than the primer sequencesand therefore have a lower melt temperature than the primers.Accordingly, the melt temperature of the amplicon produced by theprimers should also have a higher melt temperature than the probes.Thus, as the mixture cools, the re-formation of the double strandedamplicon would be expected. As previously stated, however, this is notthe case. The probes are found to preferentially bind the singlestranded amplicon members. Moreover, this preference of probe/singlestranded amplicon binding exists even when the primer sequences areadded in excess of the probes.

After the probe/single stranded amplicon member hybrids are formed, theyare detected. Standard heterogeneous assay formats are suitable fordetecting the hybrids using the detection labels and capture labelspresent on the primers and probes. The hybrids can be bound to a solidphase reagent by virtue of the capture label and detected by virtue ofthe detection label. In cases where the detection label is directlydetectable, the presence of the hybrids on the solid phase can bedetected by causing the label to produce a detectable signal, ifnecessary, and detecting the signal. In cases where the label is notdirectly detectable, the captured hybrids can be contacted with aconjugate, which generally comprises a binding member attached to adirectly detectable label. The conjugate becomes bound to the complexesand the conjugate's presence on the complexes can be detected with thedirectly detectable label. Thus, the presence of the hybrids on thesolid phase reagent can be determined. Those skilled in the art willrecognize that wash steps may be employed to wash away unhybridizedamplicon or probe as well as unbound conjugate.

In one embodiment, the heterogeneous assays can be convenientlyperformed using a solid phase support that carries an array of nucleicacid molecules. Such arrays are useful for high-throughput and/ormultiplexed assay formats. Various methods for forming such arrays frompre-formed nucleic acid molecules, or methods for generating the arrayusing in situ synthesis techniques, are generally known in the art.(See, for example, Dattagupta, et al., EP Publication No. 0 234, 726A3;Southern, U.S. Pat. No. 5,700,637; Pirrung, et al., U.S. Pat. No.5,143,854; PCT International Publication No. WO 92/10092; and, Fodor, etal., Science 251:767-777 (1991)).

Although the target sequence is described as single stranded, it also iscontemplated to include the case where the target sequence is actuallydouble stranded but is merely separated from its complement prior tohybridization with the amplification primer sequences. In the case wherePCR is employed in this method, the ends of the target sequences areusually known. In cases where LCR or a modification thereof is employedin the preferred method, the entire target sequence is usually known.Typically, the target sequence is a nucleic acid sequence such as, forexample, RNA or DNA.

The method provided herein can be used in well-known amplificationreactions that include thermal cycle reaction mixtures, particularly inPCR and gap LCR (GLCR). Amplification reactions typically employ primersto repeatedly generate copies of a target nucleic acid sequence, whichtarget sequence is usually a small region of a much larger nucleic acidsequence. Primers are themselves nucleic acid sequences that arecomplementary to regions of a target sequence. Under amplificationconditions, these primers hybridize or bind to the complementary regionsof the target sequence. Copies of the target sequence typically aregenerated by the process of primer extension and/or ligation whichutilizes enzymes with polymerase or ligase activity, separately or incombination, to add nucleotides to the hybridized primers and/or ligateadjacent probe pairs. The nucleotides that are added to the primers orprobes, as monomers or preformed oligomers, are also complementary tothe target sequence. Once the primers or probes have been sufficientlyextended and/or ligated, they are separated from the target sequence,for example, by heating the reaction mixture to a “melt temperature”which is one in which complementary nucleic acid strands dissociate.Thus, a sequence complementary to the target sequence is formed.

A new amplification cycle then can take place to further amplify thenumber of target sequences by separating any double stranded sequences,allowing primers or probes to hybridize to their respective targets,extending and/or ligating the hybridized primers or probes andre-separating. The complementary sequences that are generated byamplification cycles can serve as templates for primer extension orfilling the gap of two probes to further amplify the number of targetsequences. Typically, a reaction mixture is cycled between 20 and 100times, more typically, a reaction mixture is cycled between 25 and 50times. The numbers of cycles can be determined by the routineer. In thismanner, multiple copies of the target sequence and its complementarysequence are produced. Thus, primers initiate amplification of thetarget sequence when it is present under amplification conditions.

Generally, two primers which are complementary to a portion of a targetstrand and its complement are employed in PCR. For LCR, four probes, twoof which are complementary to a target sequence and two of which aresimilarly complementary to the target's complement, are generallyemployed. In addition to the primer sets and enzymes previouslymentioned, a nucleic acid amplification reaction mixture may alsocomprise other reagents which are well known and include but are notlimited to: enzyme cofactors such as manganese; magnesium; salts;nicotinamide adenine dinucleotide (NND); and deoxynucleotidetriphosphates (dNTPs) such as, for example, deoxyadenine triphosphate,deoxyguanine triphosphate, deoxycytosine triphosphate and deoxythyminetriphosphate.

While the amplification primers initiate amplification of the targetsequence, the detection (or hybridization) probe is not involved inamplification. Detection probes are generally nucleic acid sequences oruncharged nucleic acid analogs such as, for example, peptide nucleicacids which are disclosed in International Publication No. WO 92/20702;morpholino analogs which are described in U.S. Pat. Nos. 5,185,444,5,034,506 and 5,142,047; and the like. Depending upon the type of labelcarried by the probe, the probe is employed to capture or detect theamplicon generated by the amplification reaction. The probe is notinvolved in amplification of the target sequence and therefore may haveto be rendered “non-extendible” in that additional dNTPs cannot be addedto the probe. In and of themselves, analogs usually are non-extendibleand nucleic acid probes can be rendered non-extendible by modifying the3′ end of the probe such that the hydroxyl group is no longer capable ofparticipating in elongation. For example, the 3′ end of the probe can befunctionalized with the capture or detection label to thereby consume orotherwise block the hydroxyl group. Alternatively, the 3′ hydroxyl groupsimply can be cleaved, replaced or modified. U.S. patent applicationSer. No. 07/049,061 filed Apr. 19, 1993 and incorporated herein byreference describes modifications which can be used to render a probenon-extendible.

The ratio of primers to probes is not important. Thus, either the probesor primers can be added to the reaction mixture in excess whereby theconcentration of one would be greater than the concentration of theother. Alternatively, primers and probes can be employed in equivalentconcentrations. Preferably, however, the primers are added to thereaction mixture in excess of the probes. Thus, primer to probe ratiosof, for example, 5:1 and 20:1, are preferred.

While the length of the primers and probes can vary, the probe sequencesare selected such that they have a lower melt temperature than theprimer sequences. Hence, the primer sequences are generally longer thanthe probe sequences. Typically, the primer sequences are in the range ofbetween 20 and 50 nucleotides long, more typically in the range ofbetween 20 and 30 nucleotides long. The typical probe is in the range ofbetween 10 and 25 nucleotides long.

Various methods for synthesizing primers and probes are well known inthe art. Similarly, methods for attaching labels to primers or probesare also well known in the art. For example, it is a matter of routineto synthesize desired nucleic acid primers or probes using conventionalnucleotide phosphoramidite chemistry and instruments available fromApplied Biosystems, Inc., (Foster City, Calif.), DuPont (Wilmington,Del.), or Milligen (Bedford Mass.). Many methods have been described forlabeling oligonucleotides such as the primers or probes of the presentinvention. Enzo Biochemical (New York, N.Y.) and Clontech (Palo Alto,Calif.) both have described and commercialized probe labelingtechniques. For example, a primary amine can be attached to a 3′ oligoterminus using 3′-Amine-ON CPG™ (Clontech, Palo Alto, Calif.).Similarly, a primary amine can be attached to a 5′ oligo terminus usingAminomodifier II® (Clontech). The amines can be reacted to varioushaptens using conventional activation and linking chemistries. Inaddition, copending applications U.S. Ser. No. 625,566, filed Dec. 11,1990 and Ser. No. 630,908, filed Dec. 20, 1990, which are eachincorporated herein by reference, teach methods for labeling probes attheir 5′ and 3′ termini, respectively. International Publication Nos WO92/10505, published Jun. 25, 1992, and WO 92/11388, published Jul. 9,1992, teach methods for labeling probes at their 5′ and 3′ ends,respectively. According to one known method for labeling anoligonucleotide, a label-phosphoramidite reagent is prepared and used toadd the label to the oligonucleotide during its synthesis. See, forexample, N. T. Thuong et al., Tet. Letters 29(46):5905-5908 (1988); orJ. S. Cohen et al., published U.S. patent application Ser. No.07/246,688 (NTIS ORDER No. PAT-APPL-7-246,688) (1989). Preferably,probes are labeled at their 3′ and 5′ ends.

A capture label is attached to the primers or probes and can be aspecific binding member which forms a binding pair with the solid phasereagent's specific binding member. It will be understood that the primeror probe itself may serve as the capture label. For example, in the casewhere a solid phase reagent's binding member is a nucleic acid sequence,it may be selected such that it binds a complementary portion of theprimer or probe to thereby immobilize the primer or probe to the solidphase. In cases where the probe itself serves as the binding member,those skilled in the art will recognize that the probe will contain asequence or “tail” that is not complementary to the single strandedamplicon members. In the case where the primer itself serves as thecapture label, at least a portion of the primer will be free tohybridize with a nucleic acid on a solid phase because the probe isselected such that it is not fully complementary to the primer sequence.

Generally, probe/single stranded amplicon member complexes can bedetected using techniques commonly employed to perform heterogeneousimmunoassays. Preferably, in this embodiment, detection is performedaccording to the protocols used by the commercially available AbbottLCx® instrumentation (Abbott Laboratories, Abbott Park, Ill.).

The primers and probes disclosed herein are useful in typical PCRassays, wherein the test sample is contacted with a pair of primers,amplification is performed, the hybridization probe is added, anddetection is performed.

Another method provided by the present invention comprises contacting atest sample with a plurality of polynucleotides, wherein at least onepolynucleotide is a BS249 molecule as described herein, hybridizing thetest sample with the plurality of polynucleotides and detectinghybridization complexes. Hybridization complexes are identified andquantitated to compile a profile which is indicative of breast tissuedisease, such as breast cancer. Expressed RNA sequences may further bedetected by reverse transcription and amplification of the DNA productby procedures well-known in the art, including polymerase chain reaction(PCR).

Drug Screening and Gene Therapy

The present invention also encompasses the use of gene therapy methodsfor the introduction of anti-sense BS249 derived molecules, such aspolynucleotides or oligonucleotides of the present invention, intopatients with conditions associated with abnormal expression ofpolynucleotides related to a breast tissue disease or conditionespecially breast cancer. These molecules, including antisense RNA andDNA fragments and ribozymes, are designed to inhibit the translation ofBS249 mRNA, and may be used therapeutically in the treatment ofconditions associated with altered or abnormal expression of BS249polynucleotide.

Alternatively, the oligonucleotides described above can be delivered tocells by procedures known in the art such that the anti-sense RNA or DNAmay be expressed in vivo to inhibit production of a BS249 polypeptide inthe manner described above. Antisense constructs to a BS249polynucleotide, therefore, reverse the action of BS249 transcripts andmay be used for treating breast tissue disease conditions, such asbreast cancer. These antisense constructs may also be used to treattumor metastases.

The present invention also provides a method of screening a plurality ofcompounds for specific binding to BS249 polypeptide(s), or any fragmentthereof, to identify at least one compound which specifically binds theBS249 polypeptide. Such a method comprises the steps of providing atleast one compound; combining the BS249 polypeptide with each compoundunder suitable conditions for a time sufficient to allow binding; anddetecting the BS249 polypeptide binding to each compound.

The polypeptide or peptide fragment employed in such a test may eitherbe free in solution, affixed to a solid support, borne on a cell surfaceor located intracellularly. One method of screening utilizes eukaryoticor prokaryotic host cells which are stably transfected with recombinantnucleic acids which can express the polypeptide or peptide fragment. Adrug, compound, or any other agent may be screened against suchtransfected cells in competitive binding assays. For example, theformation of complexes between a polypeptide and the agent being testedcan be measured in either viable or fixed cells.

The present invention thus provides methods of screening for drugs,compounds, or any other agent which can be used to treat diseasesassociated with BS249. These methods comprise contacting the agent witha polypeptide or fragment thereof and assaying for either the presenceof a complex between the agent and the polypeptide, or for the presenceof a complex between the polypeptide and the cell. In competitivebinding assays, the polypeptide typically is labeled. After suitableincubation, free (or uncomplexed) polypeptide or fragment thereof isseparated from that present in bound form, and the amount of free oruncomplexed label is used as a measure of the ability of the particularagent to bind to the polypeptide or to interfere with thepolypeptide/cell complex.

The present invention also encompasses the use of competitive screeningassays in which neutralizing antibodies capable of binding polypeptidespecifically compete with a test agent for binding to the polypeptide orfragment thereof. In this manner, the antibodies can be used to detectthe presence of any polypeptide in the test sample which shares one ormore antigenic determinants with a BS249 polypeptide as provided herein.

Another technique for screening provides high throughput screening forcompounds having suitable binding affinity to at least one polypeptideof BS249 disclosed herein. Briefly, large numbers of different smallpeptide test compounds are synthesized on a solid phase, such as plasticpins or some other surface. The peptide test compounds are reacted withpolypeptide and washed. Polypeptide thus bound to the solid phase isdetected by methods well-known in the art. Purified polypeptide can alsobe coated directly onto plates for use in the screening techniquesdescribed herein. In addition, non-neutralizing antibodies can be usedto capture the polypeptide and immobilize it on the solid support. See,for example, EP 84/03564, published on Sep. 13, 1984, which isincorporated herein by reference.

The goal of rational drug design is to produce structural analogs ofbiologically active polypeptides of interest or of the small moleculesincluding agonists, antagonists, or inhibitors with which they interact.Such structural analogs can be used to design drugs which are moreactive or stable forms of the polypeptide or which enhance or interferewith the function of a polypeptide in vivo. J. Hodgson, Bio/Technology9:19-21 (1991), incorporated herein by reference.

For example, in one approach, the three-dimensional structure of apolypeptide, or of a polypeptide-inhibitor complex, is determined byx-ray crystallography, by computer modeling or, most typically, by acombination of the two approaches. Both the shape and charges of thepolypeptide must be ascertained to elucidate the structure and todetermine active site(s) of the molecule. Less often, useful informationregarding the structure of a polypeptide may be gained by modeling basedon the structure of homologous proteins. In both cases, relevantstructural information is used to design analogous polypeptide-likemolecules or to identify efficient inhibitors.

Useful examples of rational drug design may include molecules which haveimproved activity or stability as shown by S. Braxton et al.,Biochemistry 31:7796-7801 (1992), or which act as inhibitors, agonists,or antagonists of native peptides as shown by S. B. P. Athauda et al., JBiochem. (Tokyo) 113 (6):742-746 (1993), incorporated herein byreference.

It also is possible to isolate a target-specific antibody selected by anassay as described hereinabove, and then to determine its crystalstructure. In principle this approach yields a pharmacophore upon whichsubsequent drug design can be based. It further is possible to bypassprotein crystallography altogether by generating anti-idiotypicantibodies (“anti-ids”) to a functional, pharmacologically activeantibody. As a mirror image of a mirror image, the binding site of theanti-id is an analog of the original receptor. The anti-id then can beused to identify and isolate peptides from banks of chemically orbiologically produced peptides. The isolated peptides then can act asthe pharmacophore (that is, a prototype pharmaceutical drug).

A sufficient amount of a recombinant polypeptide of the presentinvention may be made available to perform analytical studies such asX-ray crystallography. In addition, knowledge of the polypeptide aminoacid sequence which is derivable from the nucleic acid sequence providedherein will provide guidance to those employing computer modelingtechniques in place of, or in addition to, x-ray crystallography.

Antibodies specific to a BS249 polypeptide (e.g., anti-BS249 antibodies)further may be used to inhibit the biological action of the polypeptideby binding to the polypeptide. In this manner, the antibodies may beused in therapy, for example, to treat breast tissue diseases includingbreast cancer and its metastases.

Further, such antibodies can detect the presence or absence of a BS249polypeptide in a test sample and, therefore, are useful as diagnosticmarkers for the diagnosis of a breast tissue disease or conditionespecially breast cancer. Such antibodies may also function as adiagnostic marker for breast tissue disease conditions, such as breastcancer.

The present invention also is directed to antagonists and inhibitors ofthe polypeptides of the present invention. The antagonists andinhibitors are those which inhibit or eliminate the function of thepolypeptide. Thus, for example, an antagonist may bind to a polypeptideof the present invention and inhibit or eliminate its function. Theantagonist, for example, could be an antibody against the polypeptidewhich eliminates the activity of a BS249 polypeptide by binding a BS249polypeptide, or in some cases the antagonist may be an oligonucleotide.Examples of small molecule inhibitors include, but are not limited to,small peptides or peptide-like molecules.

The antagonists and inhibitors may be employed as a composition with apharmaceutically acceptable carrier including, but not limited to,saline, buffered saline, dextrose, water, glycerol, ethanol andcombinations thereof. Administration of BS249 polypeptide inhibitors ispreferably systemic. The present invention also provides an antibodywhich inhibits the action of such a polypeptide.

Antisense technology can be used to reduce gene expression throughtriple-helix formation or antisense DNA or RNA, both of which methodsare based on binding of a polynucleotide to DNA or RNA. For example, the5′ coding portion of the polynucleotide sequence, which encodes for thepolypeptide of the present invention, is used to design an antisense RNAoligonucleotide of from 10 to 40 base pairs in length. A DNAoligonucleotide is designed to be complementary to a region of the geneinvolved in transcription, thereby preventing transcription and theproduction of the BS249 polypeptide. For triple helix, see, for example,Lee et al., Nuc. Acids Res. 6:3073 (1979); Cooney et al., Science241:456 (1988); and Dervan et al., Science 251:1360 (1991) The antisenseRNA oligonucleotide hybridizes to the mRNA in vivo and blockstranslation of a mRNA molecule into the BS249 polypeptide. Forantisense, see, for example, Okano, J. Neurochem. 56:560 (1991); andOligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRCPress, Boca Raton, Fla. (1988). Antisense oligonucleotides act withgreater efficacy when modified to contain artificial intemucleotidelinkages which render the molecule resistant to nucleolytic cleavage.Such artificial internucleotide linkages include, but are not limitedto, methylphosphonate, phosphorothiolate and phosphoroamydateinternucleotide linkages.

Recombinant Technology

The present invention provides host cells and expression vectorscomprising BS249 polynucleotides of the present invention and methodsfor the production of the polypeptide(s) they encode. Such methodscomprise culturing the host cells under conditions suitable for theexpression of the BS249 polynucleotide and recovering the BS249polypeptide from the cell culture.

The present invention also provides vectors which include BS249polynucleotides of the present invention, host cells which aregenetically engineered with vectors of the present invention and theproduction of polypeptides of the present invention by recombinanttechniques.

Host cells are genetically engineered (transfected, transduced ortransformed) with the vectors of this invention which may be cloningvectors or expression vectors. The vector may be in the form of aplasmid, a viral particle, a phage, etc. The engineered host cells canbe cultured in conventional nutrient media modified as appropriate foractivating promoters, selecting transfected cells, or amplifying BS249gene(s). The culture conditions, such as temperature, pH and the like,are those previously used with the host cell selected for expression,and will be apparent to the ordinarily skilled artisan.

The polynucleotides of the present invention may be employed forproducing a polypeptide by recombinant techniques. Thus, thepolynucleotide sequence may be included in any one of a variety ofexpression vehicles, in particular, vectors or plasmids for expressing apolypeptide. Such vectors include chromosomal, nonchromosomal andsynthetic DNA sequences, e.g., derivatives of SV40; bacterial plasmids;phage DNA; yeast plasmids; vectors derived from combinations of plasmidsand phage DNA, viral DNA such as vaccinia, adenovirus, fowl pox virusand pseudorabies. However, any other plasmid or vector may be used solong as it is replicable and viable in the host.

The appropriate DNA sequence may be inserted into the vector by avariety of procedures. In general, the DNA sequence is inserted intoappropriate restriction endonuclease sites by procedures known in theart. Such procedures and others are deemed to be within the scope ofthose skilled in the art. The DNA sequence in the expression vector isoperatively linked to an appropriate expression control sequence(s)(promoter) to direct mRNA synthesis. Representative examples of suchpromoters include, but are not limited to, the LTR or the SV40 promoter,the E. coli lac or trp, the phage lambda P sub L promoter and otherpromoters known to control expression of genes in prokaryotic oreukaryotic cells or their viruses. The expression vector also contains aribosome binding site for translation initiation and a transcriptionterminator. The vector may also include appropriate sequences foramplifying expression. In addition, the expression vectors preferablycontain a gene to provide a phenotypic trait for selection oftransfected host cells such as dihydrofolate reductase or neomycinresistance for eukaryotic cell culture, or such as tetracycline orampicillin resistance in E. coli.

The vector containing the appropriate DNA sequence as hereinabovedescribed, as well as an appropriate promoter or control sequence, maybe employed to transfect an appropriate host to permit the host toexpress the protein. As representative examples of appropriate hosts,there may be mentioned: bacterial cells, such as E. coli, Salmonellatyphimurium; Streptomyces sp; fungal cells, such as yeast; insect cells,such as Drosophila and Sf9; animal cells, such as CHO, COS or Bowesmelanoma; plant cells, etc. The selection of an appropriate host isdeemed to be within the scope of those skilled in the art from theteachings provided herein.

More particularly, the present invention also includes recombinantconstructs comprising one or more of the sequences as broadly describedabove. The constructs comprise a vector, such as a plasmid or viralvector, into which a sequence of the invention has been inserted, in aforward or reverse orientation. In a preferred aspect of thisembodiment, the construct further comprises regulatory sequencesincluding, for example, a promoter, operably linked to the sequence.Large numbers of suitable vectors and promoters are known to those ofskill in the art and are commercially available. The following vectorsare provided by way of example. Bacterial: pINCY (Incyte PharmaceuticalsInc., Palo Alto, Calif.), pSPORT1 (Life Technologies, Gaithersburg,Md.), pQE70, pQE60, pQE-9 (Qiagen) pBs, phagescript, psiX174,pBluescript SK, pBsKS, pNH8a, pNH16a, pNH18a, pNH46a (Stratagene);pTrc99A, pKK223-3, pKK233-3, pDR540, pRIT5 (Pharmacia); Eukaryotic:pWLneo, pSV2cat, pOG44, pXT1, pSG (Stratagene) pSVK3, pBPV, pMSG, pSVL(Pharmacia). However, any other plasmid or vector may be used as long asit is replicable and viable in the host.

Plasmid pINCY is generally identical to the plasmid pSPORT1 (availablefrom Life Technologies, Gaithersburg, Md.) with the exception that ithas two modifications in the polylinker (multiple cloning site). Thesemodifications are (1) it lacks a HindIII restriction site and (2) itsEcoRI restriction site lies at a different location. pINCY is createdfrom pSPORT1 by cleaving pSPORT1 with both HindIII and EcoRI andreplacing the excised fragment of the polylinker with synthetic DNAfragments (SEQUENCE ID NO 12 and SEQUENCE ID NO 13). This replacementmay be made in any manner known to those of ordinary skill in the art.For example, the two nucleotide sequences, SEQUENCE ID NO 12 andSEQUENCE ID NO 13, may be generated synthetically with 5′ terminalphosphates, mixed together, and then ligated under standard conditionsfor performing staggered end ligations into the pSPORT1 plasmid cut withHindIII and EcoRI. Suitable host cells (such as E. coli DH5μ cells) thenare transfected with the ligated DNA and recombinant clones are selectedfor ampicillin resistance. Plasmid DNA then is prepared from individualclones and subjected to restriction enzyme analysis or DNA sequencing inorder to confirm the presence of insert sequences in the properorientation. Other cloning strategies known to the ordinary artisan alsomay be employed.

Promoter regions can be selected from any desired gene using CAT(chloramphenicol transferase) vectors or other vectors with selectablemarkers. Two appropriate vectors are pKK232-8 and pCM7. Particular namedbacterial promoters include lacd, lacZ, T3, SP6, T7, gpt, lambda P subR, P sub L and trp. Eukaryotic promoters include cytomegalovirus (CMV)immediate early, herpes simplex virus (HSV) thymidine kinase, early andlate SV40, LTRs from retroviruses and mouse metallothionein-I. Selectionof the appropriate vector and promoter is well within the level ofordinary skill in the art.

In a further embodiment, the present invention provides host cellscontaining the above-described construct. The host cell can be a highereukaryotic cell, such as a mammalian cell, or a lower eukaryotic cell,such as a yeast cell, or the host cell can be a prokaryotic cell, suchas a bacterial cell. Introduction of the construct into the host cellcan be effected by calcium phosphate transfection, DEAE-Dextran mediatedtransfection, or electroporation [L. Davis et al., Basic Methods inMolecular Biology, 2nd edition, Appleton and Lang, Paramount Publishing,East Norwalk, Conn. (1994)].

The constructs in host cells can be used in a conventional manner toproduce the gene product encoded by the recombinant sequence.Alternatively, the polypeptides of the invention can be syntheticallyproduced by conventional peptide synthesizers.

Recombinant proteins can be expressed in mammalian cells, yeast,bacteria, or other cells, under the control of appropriate promoters.Cell-free translation systems can also be employed to produce suchproteins using RNAs derived from the DNA constructs of the presentinvention. Appropriate cloning and expression vectors for use withprokaryotic and eukaryotic hosts are described by Sambrook et al.,Molecular Cloning: A Laboratory Manual, Second Edition, (Cold SpringHarbor, N.Y., 1989), which is hereby incorporated by reference.

Transcription of a DNA encoding the polypeptide(s) of the presentinvention by higher eukaryotes is increased by inserting an enhancersequence into the vector. Enhancers are cis-acting elements of DNA,usually about from 10 to 300 bp, that act on a promoter to increase itstranscription. Examples include the SV40 enhancer on the late side ofthe replication origin (bp 100 to 270), a cytomegalovirus early promoterenhancer, a polyoma enhancer on the late side of the replication originand adenovirus enhancers.

Generally, recombinant expression vectors will include origins ofreplication and selectable markers permitting transfection of the hostcell, e.g., the ampicillin resistance gene of E. coli and S. cerevisiaeTRP1 gene, and a promoter derived from a highly-expressed gene to directtranscription of a downstream structural sequence. Such promoters can bederived from operons encoding glycolytic enzymes such as3-phosphoglycerate kinase (PGK), alpha factor, acid phosphatase, or heatshock proteins, among others. The heterologous structural sequence isassembled in appropriate phase with translation initiation andtermination sequences, and preferably, a leader sequence capable ofdirecting secretion of translated protein into the periplasmic space orextracellular medium. Optionally, the heterologous sequence can encode afusion protein including an N-terminal identification peptide impartingdesired characteristics, e.g., stabilization or simplified purificationof expressed recombinant product.

Useful expression vectors for bacterial use are constructed by insertinga structural DNA sequence encoding a desired protein together withsuitable translation initiation and termination signals in operablereading phase with a functional promoter. The vector will comprise oneor more phenotypic selectable markers and an origin of replication toensure maintenance of the vector and to, if desirable, provideamplification within the host. Suitable prokaryotic hosts fortransfection include E. coli, Bacillus subtilis, Salmonella typhimuriumand various species within the genera Pseudomonas, Streptomyces andStaphylococcus, although others may also be employed as a routine matterof choice.

Useful expression vectors for bacterial use comprise a selectable markerand bacterial origin of replication derived from plasmids comprisinggenetic elements of the well-known cloning vector pBR322 (ATCC 37017).Other vectors include but are not limited to PKK223-3 (Pharmacia FineChemicals, Uppsala, Sweden) and GEM1 (Promega Biotec, Madison, Wis.).These pBR322 “backbone” sections are combined with an appropriatepromoter and the structural sequence to be expressed.

Following transfection of a suitable host and growth of the host to anappropriate cell density, the selected promoter is derepressed byappropriate means (e.g., temperature shift or chemical induction), andcells are cultured for an additional period. Cells are typicallyharvested by centrifugation, disrupted by physical or chemical means,and the resulting crude extract retained for further purification.Microbial cells employed in expression of proteins can be disrupted byany convenient method including freeze-thaw cycling, sonication,mechanical disruption, or use of cell lysing agents. Such methods arewell-known to the ordinary artisan.

Various mammalian cell culture systems can also be employed to expressrecombinant protein. Examples of mammalian expression systems includethe COS-7 lines of monkey kidney fibroblasts described by Gluzman, Cell23:175 (1981), and other cell lines capable of expressing a compatiblevector, such as the C127, HEK-293, 3T3, CHO, HeLa and BHK cell lines.Mammalian expression vectors will comprise an origin of replication, asuitable promoter and enhancer and also any necessary ribosome bindingsites, polyadenylation sites, splice donor and acceptor sites,transcriptional termination sequences and 5′ flanking nontranscribedsequences. DNA sequences derived from the SV40 viral genome, forexample, SV40 origin, early promoter, enhancer, splice, andpolyadenylation sites may be used to provide the required nontranscribedgenetic elements. Representative, useful vectors include pRc/CMV andpcDNA3 (available from Invitrogen, San Diego, Calif.).

BS249 polypeptides are recovered and purified from recombinant cellcultures by known methods including affinity chromatography, ammoniumsulfate or ethanol precipitation, acid extraction, anion or cationexchange chromatography, phosphocellulose chromatography, hydrophobicinteraction chromatography, hydroxyapatite chromatography or lectinchromatography. It is preferred to have low concentrations(approximately 0.1-5 mM) of calcium ion present during purification[Price, et al., J. Biol. Chem. 244:917 (1969)]. Protein refolding stepscan be used, as necessary, in completing configuration of thepolypeptide. Finally, high performance liquid chromatography (HPLC) canbe employed for final purification steps.

Thus, polypeptides of the present invention may be naturally purifiedproducts expressed from a high expressing cell line, or a product ofchemical synthetic procedures, or produced by recombinant techniquesfrom a prokaryotic or eukaryotic host (for example, by bacterial, yeast,higher plant, insect and mammalian cells in culture). Depending upon thehost employed in a recombinant production procedure, the polypeptides ofthe present invention may be glycosylated with mammalian or othereukaryotic carbohydrates or may be non-glycosylated. The polypeptides ofthe invention may also include an initial methionine amino acid residue.

The starting plasmids can be constructed from available plasmids inaccord with published, known procedures. In addition, equivalentplasmids to those described are known in the art and will be apparent toone of ordinary skill in the art.

The following is the general procedure for the isolation and analysis ofcDNA clones. In a particular embodiment disclosed herein, mRNA isisolated from breast tissue and used to generate the cDNA library.Breast tissue is obtained from patients by surgical resection and isclassified as tumor or non-tumor tissue by a pathologist.

The cDNA inserts from random isolates of the breast tissue libraries aresequenced in part, analyzed in detail as set forth in the Examples, andare disclosed in the Sequence Listing as SEQUENCE ID NOS 1-9. Alsoanalyzed in detail as set forth in the Examples, and disclosed in theSequence Listing, is the full-length sequence of clone 3769673 [referredto herein as 3769673inh (SEQUENCE ID NO 10)]. The consensus sequence ofthese inserts is presented as SEQUENCE ID NO 11. These polynucleotidesmay contain an entire open reading frame with or without associatedregulatory sequences for a particular gene, or they may encode only aportion of the gene of interest. This is attributed to the fact thatmany genes are several hundred and sometimes several thousand bases inlength and, with current technology, cannot be cloned in their entiretybecause of vector limitations, incomplete reverse transcription of thefirst strand, or incomplete replication of the second strand.Contiguous, secondary clones containing additional nucleotide sequencesmay be obtained using a variety of methods known to those of skill inthe art.

Methods for DNA sequencing are well known in the art. Conventionalenzymatic methods employ DNA polymerase, Klenow fragment, Sequenase (USBiochemical Corp, Cleveland, Ohio) or Taq polymerase to extend DNAchains from an oligonucleotide primer annealed to the DNA template ofinterest. Methods have been developed for the use of bothsingle-stranded and double-stranded templates. The chain terminationreaction products may be electrophoresed on urea/polyacrylamide gels anddetected either by autoradiography (for radionucleotide labeledprecursors) or by fluorescence (for fluorescent-labeled precursors).Recent improvements in mechanized reaction preparation, sequencing andanalysis using the fluorescent detection method have permitted expansionin the number of sequences that can be determined per day using machinessuch as the Applied Biosystems 377 DNA Sequencers (Applied Biosystems,Foster City, Calif.).

The reading frame of the nucleotide sequence can be ascertained byseveral types of analyses. First, reading frames contained within thecoding sequence can be analyzed for the presence of start codon ATG andstop codons TGA, TAA or TAG. Typically, one reading frame will continuethroughout the major portion of a cDNA sequence while other readingframes tend to contain numerous stop codons. In such cases, readingframe determination is straightforward. In other more difficult cases,further analysis is required.

Algorithms have been created to analyze the occurrence of individualnucleotide bases at each putative codon triplet. See, for example J. W.Fickett, Nuc. Acids Res. 10:5303 (1982). Coding DNA for particularorganisms (bacteria, plants and animals) tends to contain certainnucleotides within certain triplet periodicities, such as a significantpreference for pyrimidines in the third codon position. Thesepreferences have been incorporated into widely available software whichcan be used to determine coding potential (and frame) of a given stretchof DNA. The algorithm-derived information combined with start/stop codoninformation can be used to determine proper frame with a high degree ofcertainty. This, in turn, readily permits cloning of the sequence in thecorrect reading frame into appropriate expression vectors.

The nucleic acid sequences disclosed herein may be joined to a varietyof other polynucleotide sequences and vectors of interest by means ofwell-established recombinant DNA techniques. See J. Sambrook et al.,supra. Vectors of interest include cloning vectors, such as plasmids,cosmids, phage derivatives, phagemids, as well as sequencing,replication and expression vectors, and the like. In general, suchvectors contain an origin of replication functional in at least oneorganism, convenient restriction endonuclease digestion sites andselectable markers appropriate for particular host cells. The vectorscan be transferred by a variety of means known to those of skill in theart into suitable host cells which then produce the desired DNA, RNA orpolypeptides.

Occasionally, sequencing or random reverse transcription errors willmask the presence of the appropriate open reading frame or regulatoryelement. In such cases, it is possible to determine the correct readingframe by attempting to express the polypeptide and determining the aminoacid sequence by standard peptide mapping and sequencing techniques.See, F. M. Ausubel et al., Current Protocols in Molecular Biology, JohnWiley & Sons, New York, N.Y. (1989). Additionally, the actual readingframe of a given nucleotide sequence may be determined by transfectionof host cells with vectors containing all three potential readingframes. Only those cells with the nucleotide sequence in the correctreading frame will produce a peptide of the predicted length.

The nucleotide sequences provided herein have been prepared by current,state-of-the-art, automated methods and, as such, may containunidentified nucleotides. These will not present a problem to thoseskilled in the art who wish to practice the invention. Several methodsemploying standard recombinant techniques, described in J. Sambrook(supra) or periodic updates thereof, may be used to complete the missingsequence information. The same techniques used for obtaining a fulllength sequence, as described herein, may be used to obtain nucleotidesequences.

Expression of a particular cDNA may be accomplished by subcloning thecDNA into an appropriate expression vector and transfecting this vectorinto an appropriate expression host. The cloning vector used for thegeneration of the breast tissue cDNA library can be used fortranscribing mRNA of a particular cDNA and contains a promoter forbeta-galactosidase, an amino-terminal met and the subsequent seven aminoacid residues of beta-galactosidase. Immmediately following these eightresidues is an engineered bacteriophage promoter useful for artificialpriming and transcription, as well as a number of unique restrictionsites, including EcoRI, for cloning. The vector can be transfected intoan appropriate host strain of E. coli.

Induction of the isolated bacterial strain with isopropylthiogalactoside(IPTG) using standard methods will produce a fusion protein whichcontains the first seven residues of beta-galactosidase, about 15residues of linker and the peptide encoded within the cDNA. Since cDNAclone inserts are generated by an essentially random process, there isone chance in three that the included cDNA will lie in the correct framefor proper translation. If the cDNA is not in the proper reading frame,the correct frame can be obtained by deletion or insertion of anappropriate number of bases by well known methods including in vitromutagenesis, digestion with exonuclease III or mung bean nuclease, oroligonucleotide linker inclusion.

The cDNA can be shuttled into other vectors known to be useful forexpression of protein in specific hosts. Oligonucleotide primerscontaining cloning sites and segments of DNA sufficient to hybridize tostretches at both ends of the target cDNA can be synthesized chemicallyby standard methods. These primers can then be used to amplify thedesired gene segments by PCR. The resulting new gene segments can bedigested with appropriate restriction enzymes under standard conditionsand isolated by gel electrophoresis. Alternately, similar gene segmentscan be produced by digestion of the cDNA with appropriate restrictionenzymes and filling in the missing gene segments with chemicallysynthesized oligonucleotides. Segments of the coding sequence from morethan one gene can be ligated together and cloned in appropriate vectorsto optimize expression of recombinant sequence.

Suitable expression hosts for such chimeric molecules include, but arenot limited to, mammalian cells, such as Chinese Hamster Ovary (CHO) andhuman embryonic kidney (HEK) 293 cells, insect cells, such as Sf9 cells,yeast cells, such as Saccharomyces cerevisiae and bacteria, such as E.coli. For each of these cell systems, a useful expression vector mayalso include an origin of replication to allow propagation in bacteriaand a selectable marker such as the beta-lactamase antibiotic resistancegene to allow selection in bacteria. In addition, the vectors mayinclude a second selectable marker, such as the neomycinphosphotransferase gene, to allow selection in transfected eukaryotichost cells. Vectors for use in eukaryotic expression hosts may requirethe addition of 3′ poly A tail if the sequence of interest lacks poly A.

Additionally, the vector may contain promoters or enhancers whichincrease gene expression. Such promoters are host specific and include,but are not limited to, MMTV, SV40, or metallothionine promoters for CHOcells; trp, lac, tac or T7 promoters for bacterial hosts; or alphafactor, alcohol oxidase or PGH promoters for yeast. Adenoviral vectorswith or without transcription enhancers, such as the Rous sarcoma virus(RSV) enhancer, may be used to drive protein expression in mammaliancell lines. Once homogeneous cultures of recombinant cells are obtained,large quantities of recombinantly produced protein can be recovered fromthe conditioned medium and analyzed using chromatographic methods wellknown in the art. An alternative method for the production of largeamounts of secreted protein involves the transfection of mammalianembryos and the recovery of the recombinant protein from milk producedby transgenic cows, goats, sheep, etc. Polypeptides and closely relatedmolecules may be expressed recombinantly in such a way as to facilitateprotein purification. One approach involves expression of a chimericprotein which includes one or more additional polypeptide domains notnaturally present on human polypeptides. Such purification-facilitatingdomains include, but are not limited to, metal-chelating peptides suchas histidine-tryptophan domains that allow purification on immobilizedmetals, protein A domains that allow purification on immobilizedimmunoglobulin and the domain utilized in the FLAGS extension/affinitypurification system (Immunex Corp, Seattle, Wash.). The inclusion of acleavable linker sequence such as Factor XA or enterokinase fromInvitrogen (San Diego, Calif.) between the polypeptide sequence and thepurification domain may be useful for recovering the polypeptide.

Immunoassays

BS249 polypeptides, including fragments, derivatives, and analogsthereof, or cells expressing such polypeptides, can be utilized in avariety of assays, many of which are described herein, for the detectionof antibodies to breast tissue. They also can be used as immunogens toproduce antibodies. These antibodies can be, for example, polyclonal ormonoclonal antibodies, chimeric, single chain and humanized antibodies,as well as Fab fragments, or the product of an Fab expression library.Various procedures known in the art may be used for the production ofsuch antibodies and fragments.

For example, antibodies generated against a polypeptide comprising asequence of the present invention can be obtained by direct injection ofthe polypeptide into an animal or by administering the polypeptide to ananimal such as a mouse, rabbit, goat or human. A mouse, rabbit or goatis preferred. The polypeptide is selected from the group consisting ofSEQUENCE ID NO 23, SEQUENCE ID NO 24, SEQUENCE ID NO 25, SEQUENCE ID NO26, SEQUENCE ID NO 27, and fragments thereof. The antibody so obtainedthen will bind the polypeptide itself. In this manner, even a sequenceencoding only a fragment of the polypeptide can be used to generateantibodies that bind the native polypeptide. Such antibodies then can beused to isolate the polypeptide from test samples such as tissuesuspected of containing that polypeptide. For preparation of monoclonalantibodies, any technique which provides antibodies produced bycontinuous cell line cultures can be used. Examples include thehybridoma technique as described by Kohler and Milstein, Nature256:495-497 (1975), the trioma technique, the human B-cell hybridomatechnique as described by Kozbor et al., Immun. Today 4:72 (1983) andthe EBV-hybridoma technique to produce human monoclonal antibodies asdescribed by Cole et al., in Monoclonal Antibodies and Cancer Therapy,Alan R. Liss, Inc, New York, N.Y., pp. 77-96 (1985). Techniquesdescribed for the production of single chain antibodies can be adaptedto produce single chain antibodies to immunogenic polypeptide productsof this invention. See, for example, U.S. Pat. No. 4,946,778, which isincorporated herein by reference.

Various assay formats may utilize the antibodies of the presentinvention, including “sandwich” immunoassays and probe assays. Forexample, the antibodies of the present invention, or fragments thereof,can be employed in various assay systems to determine the presence, ifany, of BS249 antigen in a test sample. For example, in a first assayformat, a polyclonal or monoclonal antibody or fragment thereof, or acombination of these antibodies, which has been coated on a solid phase,is contacted with a test sample, to form a first mixture. This firstmixture is incubated for a time and under conditions sufficient to formantigen/antibody complexes. Then, an indicator reagent comprising amonoclonal or a polyclonal antibody or a fragment thereof, or acombination of these antibodies, to which a signal generating compoundhas been attached, is contacted with the antigen/antibody complexes toform a second mixture. This second mixture then is incubated for a timeand under conditions sufficient to form antibody/antigen/antibodycomplexes. The presence of BS249 antigen in the test sample and capturedon the solid phase, if any, is determined by detecting the measurablesignal generated by the signal generating compound. The amount of BS249antigen present in the test sample is proportional to the signalgenerated.

In an alternative assay format, a mixture is formed by contacting: (1) apolyclonal antibody, monoclonal antibody, or fragment thereof, whichspecifically binds to BS249 antigen, or a combination of such antibodiesbound to a solid support; (2) the test sample; and (3) an indicatorreagent comprising a monoclonal antibody, polyclonal antibody, orfragment thereof, which specifically binds to a different BS249 antigen(or a combination of these antibodies) to which a signal generatingcompound is attached. This mixture is incubated for a time and underconditions sufficient to form antibody/antigen/antibody complexes. Thepresence, if any, of BS249 antigen present in the test sample andcaptured on the solid phase is determined by detecting the measurablesignal generated by the signal generating compound. The amount of BS249antigen present in the test sample is proportional to the signalgenerated.

In another assay format, one or a combination of at least two monoclonalantibodies of the invention can be employed as a competitive probe forthe detection of antibodies to BS249 antigen. For example, BS249polypeptides such as the recombinant antigens disclosed herein, eitheralone or in combination, are coated on a solid phase. A test samplesuspected of containing antibody to BS249 antigen then is incubated withan indicator reagent comprising a signal generating compound and atleast one monoclonal antibody of the invention for a time and underconditions sufficient to form antigen/antibody complexes of either thetest sample and indicator reagent bound to the solid phase or theindicator reagent bound to the solid phase. The reduction in binding ofthe monoclonal antibody to the solid phase can be quantitativelymeasured.

In yet another detection method, each of the monoclonal or polyclonalantibodies of the present invention can be employed in the detection ofBS249 antigens in tissue sections, as well as in cells, byinmnunohistochemical analysis. The tissue sections can be cut fromeither frozen or chemically fixed samples of tissue. If the antigens areto be detected in cells, the cells can be isolated from blood, urine,breast aspirates, or other bodily fluids. The cells may be obtained bybiopsy, either surgical or by needle. The cells can be isolated bycentrifugation or magnetic attraction after labeling with magneticparticles or ferrofluids so as to enrich a particular fraction of cellsfor staining with the antibodies of the present invention. Cytochemicalanalysis wherein these antibodies are labeled directly (with, forexample, fluorescein, colloidal gold, horseradish peroxidase, alkalinephosphatase, etc.) or are labeled by using secondary labeledanti-species antibodies (with various labels as exemplified herein) totrack the histopathology of disease also are within the scope of thepresent invention.

In addition, these monoclonal antibodies can be bound to matricessimilar to CNBr-activated Sepharose and used for the affinitypurification of specific BS249 polypeptides from cell cultures orbiological tissues such as to purify recombinant and native BS249proteins.

The monoclonal antibodies of the invention also can be used for thegeneration of chimeric antibodies for therapeutic use, or other similarapplications.

The monoclonal antibodies or fragments thereof can be providedindividually to detect BS249 antigens. Combinations of the monoclonalantibodies (and fragments thereof) provided herein also may be usedtogether as components in a mixture or “cocktail” of at least one BS249antibody of the invention, along with antibodies which specifically bindto other BS249 regions, each antibody having different bindingspecificities. Thus, this cocktail can include the monoclonal antibodiesof the invention which are directed to BS249 polypeptides disclosedherein and other monoclonal antibodies specific to other antigenicdeterminants of BS249 antigens or other related proteins.

The polyclonal antibody or fragment thereof which can be used in theassay formats should specifically bind to a BS249 polypeptide or otherBS249 polypeptides additionally used in the assay. The polyclonalantibody used preferably is of mammalian origin such as, human, goat,rabbit or sheep polyclonal antibody which binds BS249 polypeptide. Mostpreferably, the polyclonal antibody is of rabbit origin. The polyclonalantibodies used in the assays can be used either alone or as a cocktailof polyclonal antibodies. Since the cocktails used in the assay formatsare comprised of either monoclonal antibodies or polyclonal antibodieshaving different binding specificity to BS249 polypeptides, they areuseful for the detecting, diagnosing, staging, monitoring,prognosticating, in vivo imaging, preventing or treating, or determiningthe predisposition to, diseases and conditions of the breast, such asbreast cancer.

It is contemplated and within the scope of the present invention thatBS249 antigen may be detectable in assays by use of a recombinantantigen as well as by use of a synthetic peptide or purified peptide,which peptide comprises an amino acid sequence of BS249. The amino acidsequence of such a polypeptide is selected from the group consisting ofSEQUENCE ID NO 23, SEQUENCE ID NO 24, SEQUENCE ID NO 25, SEQUENCE ID NO26, SEQUENCE ID NO 27, and fragments thereof. It also is within thescope of the present invention that different synthetic, recombinant orpurified peptides, identifying different epitopes of BS249, can be usedin combination in an assay for the detecting, diagnosing, staging,monitoring, prognosticating, in vivo imaging, preventing or treating, ordetermining the predisposition to diseases and conditions of the breast,such as breast cancer. In this case, all of these peptides can be coatedonto one solid phase; or each separate peptide may be coated ontoseparate solid phases, such as microparticles, and then combined to forma mixture of peptides which can be later used in assays. Furthermore, itis contemplated that multiple peptides which define epitopes fromdifferent antigens may be used for the detection, diagnosis, staging,monitoring, prognosis, prevention or treatment of, or determining thepredisposition to, diseases and conditions of the breast, such as breastcancer. Peptides coated on solid phases or labeled with detectablelabels are then allowed to compete with those present in a patientsample (if any) for a limited amount of antibody. A reduction in bindingof the synthetic, recombinant, or purified peptides to the antibody (orantibodies) is an indication of the presence of BS249 antigen in thepatient sample. The presence of BS249 antigen indicates the presence ofbreast tissue disease, especially breast cancer, in the patient.Variations of assay formats are known to those of ordinary skill in theart and many are discussed herein below.

In another assay format, the presence of anti-BS249 antibody and/orBS249 antigen can be detected in a simultaneous assay, as follows. Atest sample is simultaneously contacted with a capture reagent of afirst analyte, wherein said capture reagent comprises a first bindingmember specific for a first analyte attached to a solid phase and acapture reagent for a second analyte, wherein said capture reagentcomprises a first binding member for a second analyte attached to asecond solid phase, to thereby form a mixture. This mixture is incubatedfor a time and under conditions sufficient to form capture reagent/firstanalyte and capture reagent/second analyte complexes. These so-formedcomplexes then are contacted with an indicator reagent comprising amember of a binding pair specific for the first analyte labeled with asignal generating compound and an indicator reagent comprising a memberof a binding pair specific for the second analyte labeled with a signalgenerating compound to form a second mixture. This second mixture isincubated for a time and under conditions sufficient to form capturereagent/first analyte/indicator reagent complexes and capturereagent/second analyte/indicator reagent complexes. The presence of oneor more analytes is determined by detecting a signal generated inconnection with the complexes formed on either or both solid phases asan indication of the presence of one or more analytes in the testsample. In this assay format, recombinant antigens derived from theexpression systems disclosed herein may be utilized, as well asmonoclonal antibodies produced from the proteins derived from theexpression systems as disclosed herein. For example, in this assaysystem, BS249 antigen can be the first analyte. Such assay systems aredescribed in greater detail in EP Publication No. 0473065.

In yet other assay formats, the polypeptides disclosed herein may beutilized to detect the presence of antibody against BS249 antigen intest samples. For example, a test sample is incubated with a solid phaseto which at least one polypeptide such as a recombinant protein orsynthetic peptide has been attached. The polypeptide is selected fromthe group consisting of SEQUENCE ID NO 23, SEQUENCE ID NO 24, SEQUENCEID NO 25, SEQUENCE ID NO 26, SEQUENCE ID NO 27, and fragments thereof.These are reacted for a time and under conditions sufficient to formantigen/antibody complexes. Following incubation, the antigen/antibodycomplex is detected. Indicator reagents may be used to facilitatedetection, depending upon the assay system chosen. In another assayformat, a test sample is contacted with a solid phase to which arecombinant protein produced as described herein is attached, and alsois contacted with a monoclonal or polyclonal antibody specific for theprotein, which preferably has been labeled with an indicator reagent.After incubation for a time and under conditions sufficient forantibody/antigen complexes to form, the solid phase is separated fromthe free phase, and the label is detected in either the solid or freephase as an indication of the presence of antibody against BS249antigen. Other assay formats utilizing the recombinant antigensdisclosed herein are contemplated. These include contacting a testsample with a solid phase to which at least one antigen from a firstsource has been attached, incubating the solid phase and test sample fora time and under conditions sufficient to form antigen/antibodycomplexes, and then contacting the solid phase with a labeled antigen,which antigen is derived from a second source different from the firstsource. For example, a recombinant protein derived from a first sourcesuch as E. coli is used as a capture antigen on a solid phase, a testsample is added to the so-prepared solid phase, and following standardincubation and washing steps as deemed or required, a recombinantprotein derived from a different source (i.e., non-E. coli ) is utilizedas a part of an indicator reagent which subsequently is detected.Likewise, combinations of a recombinant antigen on a solid phase andsynthetic peptide in the indicator phase also are possible. Any assayformat which utilizes an antigen specific for BS249 produced or derivedfrom a first source as the capture antigen and an antigen specific forBS249 from a different second source is contemplated. Thus, variouscombinations of recombinant antigens, as well as the use of syntheticpeptides, purified proteins and the like, are within the scope of thisinvention. Assays such as this and others are described in U.S. Pat. No.5,254,458, which enjoys common ownership and is incorporated herein byreference.

Other embodiments which utilize various other solid phases also arecontemplated and are within the scope of this invention. For example,ion capture procedures for immobilizing an immobilizable reactioncomplex with a negatively charged polymer (described in EP publication0326100 and EP publication No. 0406473), can be employed according tothe present invention to effect a fast solution-phase immunochemicalreaction. An immobilizable immune complex is separated from the rest ofthe reaction mixture by ionic interactions between the negativelycharged poly-anion/immune complex and the previously treated, positivelycharged porous matrix and detected by using various signal generatingsystems previously described, including those described inchemiluminescent signal measurements as described in EPO Publication No.0 273,115.

Also, the methods of the present invention can be adapted for use insystems which utilize microparticle technology including automated andsemi-automated systems wherein the solid phase comprises a microparticle(magnetic or non-magnetic). Such systems include those described in, forexample, published EPO applications Nos. EP 0 425 633 and EP 0 424 634,respectively.

The use of scanning probe microscopy (SPM) for immunoassays also is atechnology to which the monoclonal antibodies of the present inventionare easily adaptable. In scanning probe microscopy, particularly inatomic force microscopy, the capture phase, for example, at least one ofthe monoclonal antibodies of the invention, is adhered to a solid phaseand a scanning probe microscope is utilized to detect antigen/antibodycomplexes which may be present on the surface of the solid phase. Theuse of scanning tunneling microscopy eliminates the need for labelswhich normally must be utilized in many immunoassay systems to detectantigen/antibody complexes. The use of SPM to monitor specific bindingreactions can occur in many ways. In one embodiment, one member of aspecific binding partner (analyte specific substance which is themonoclonal antibody of the invention) is attached to a surface suitablefor scanning. The attachment of the analyte specific substance may be byadsorption to a test piece which comprises a solid phase of a plastic ormetal surface, following methods known to those of ordinary skill in theart. Or, covalent attachment of a specific binding partner (analytespecific substance) to a test piece which test piece comprises a solidphase of derivatized plastic, metal, silicon, or glass may be utilized.Covalent attachment methods are known to those skilled in the art andinclude a variety of means to irreversibly link specific bindingpartners to the test piece. If the test piece is silicon or glass, thesurface must be activated prior to attaching the specific bindingpartner. Also, polyelectrolyte interactions may be used to immobilize aspecific binding partner on a surface of a test piece by usingtechniques and chemistries. The preferred method of attachment is bycovalent means. Following attachment of a specific binding member, thesurface may be further treated with materials such as serum, proteins,or other blocking agents to minimize non-specific binding. The surfacealso may be scanned either at the site of manufacture or point of use toverify its suitability for assay purposes. The scanning process is notanticipated to alter the specific binding properties of the test piece.

While the present invention discloses the preference for the use ofsolid phases, it is contemplated that the reagents such as antibodies,proteins and peptides of the present invention can be utilized innon-solid phase assay systems. These assay systems are known to thoseskilled in the art, and are considered to be within the scope of thepresent invention.

It is contemplated that the reagent employed for the assay can beprovided in the form of a test kit with one or more containers such asvials or bottles, with each container containing a separate reagent suchas a probe, primer, monoclonal antibody or a cocktail of monoclonalantibodies, or a polypeptide (e.g. recombinantly, synthetically producedor purified) employed in the assay. The polypeptide is selected from thegroup consisting of SEQUENCE ID NO 23, SEQUENCE ID NO 24, SEQUENCE ID NO25, SEQUENCE ID NO 26, SEQUENCE ID NO 27, and fragments thereof. Othercomponents such as buffers, controls and the like, known to those ofordinary skill in art, may be included in such test kits. It also iscontemplated to provide test kits which have means for collecting testsamples comprising accessible body fluids, e.g., blood, urine, salivaand stool. Such tools useful for collection (“collection materials”)include lancets and absorbent paper or cloth for collecting andstabilizing blood; swabs for collecting and stabilizing saliva; cups forcollecting and stabilizing urine or stool samples. Collection materials,papers, cloths, swabs, cups and the like, may optionally be treated toavoid denaturation or irreversible adsorption of the sample. Thecollection materials also may be treated with or contain preservatives,stabilizers or antimicrobial agents to help maintain the integrity ofthe specimens. Test kits designed for the collection, stabilization andpreservation of test specimens obtained by surgery or needle biopsy arealso useful. It is contemplated that all kits may be configured in twocomponents which can be provided separately; one component forcollection and transport of the specimen and the other component for theanalysis of the specimen. The collection component, for example, can beprovided to the open market user while the components for analysis canbe provided to others such as laboratory personnel for determination ofthe presence, absence or amount of analyte. Further, kits for thecollection, stabilization and preservation of test specimens may beconfigured for use by untrained personnel and may be available in theopen market for use at home with subsequent transportation to alaboratory for analysis of the test sample.

In Vivo Antibody Use

Antibodies of the present invention can be used in vivo; that is, theycan be injected into patients suspected of having or having diseases ofthe breast for diagnostic or therapeutic uses. The use of antibodies forin vivo diagnosis is well known in the art. Sumerdon et al., Nucl. Med.Biol 17:247-254 (1990) have described an optimized antibody-chelator forthe radioimmunoscintographic imaging of carcinoembryonic antigen (CEA)expressing tumors using Indium-111 as the label. Griffin et al., J ClinOnc 9:631-640 (1991) have described the use of this agent in detectingtumors in patients suspected of having recurrent colorectal cancer. Theuse of similar agents with paramagnetic ions as labels for magneticresonance imaging is know in the art (R. B. Lauffer, Magnetic Resonancein Medicine 22:339-342 (1991). It is anticipated that antibodiesdirected against BS249 antigen can be injected into patients suspectedof having a disease of the breast such as breast cancer for the purposeof diagnosing or staging the disease status of the patient. The labelused will depend on the imaging modality chosen. Radioactive labels suchas Indium-111, Technetium-99m, or Iodine-131 can be used for planarscans or single photon emission computed tomography (SPECT). Positronemitting labels such as Fluorine-19 can also be used for positronemission tomography (PET). For MRI, paramagnetic ions such as Gadolinium(III) or Manganese (II) can be used. Localization of the label withinthe breast or external to the breast may allow determination of spreadof the disease. The amount of label within the breast may allowdetermination of the presence or absence of cancer of the breast.

For patients known to have a disease of the breast, injection of anantibody directed against BS249 antigen may have therapeutic benefit.The antibody may exert its effect without the use of attached agents bybinding to BS249 antigen expressed on or in the tissue or organ.Alternatively, the antibody may be conjugated to cytotoxic agents suchas drugs, toxins, or radionuclides to enhance its therapeutic effect.Garnett and Baldwin, Cancer Research 46:2407-2412 (1986) have describedthe preparation of a drug-monoclonal antibody conjugate. Pastan et al.,Cell 47:641-648 (1986) have reviewed the use of toxins conjugated tomonoclonal antibodies for the therapy of various cancers. Goodwin andMeares, Cancer Supplement 80:2675-2680 (1997) have described the use ofYittrium-90 labeled monoclonal antibodies in various strategies tomaximize the dose to tumor while limiting normal tissue toxicity. Otherknown cytotoxic radionuclides include Copper-67, Iodine-131, andRhenium-186 all of which can be used to label monoclonal antibodiesdirected against BS249 antigen for the treatment of cancer of thebreast.

E. coli bacteria (clone 3769673) was deposited on Mar. 9, 1998 with theAmerican Type Culture Collection (A.T.C.C.), 10801 University Blvd.Manassas, Va., 20110. The deposit was made under the terms of theBudapest Treaty and will be maintained for a period of thirty (30) yearsfrom the date of deposit, or for five (5) years after the last requestfor the deposit, or for the enforceable period of the U.S. patent,whichever is longer. The deposit and any other deposited materialdescribed herein are provided for convenience only, and are not requiredto practice the present invention in view of the teachings providedherein. The cDNA sequence in all of the deposited material isincorporated herein by reference. Clone 3769673 was accorded A.T.C.C.Deposit No. 98679.

The present invention will now be described by way of examples, whichare meant to illustrate, but not to limit, the scope of the presentinvention.

EXAMPLES Example 1 Identification of Breast Tissue Library BS249Gene-Specific Clones

A. Library Comparison of Expressed Sequence Tags (EST's) or TranscriptImages. Partial sequences of cDNA clone inserts, so-called “expressedsequence tags” (EST's), were derived from cDNA libraries made frombreast tumor tissues, breast non-tumor tissues and numerous othertissues, both tumor and non-tumor and entered into a database (LIFESEQ™database, available from Incyte Pharmaceuticals, Palo Alto, Calif.) asgene transcript images. See International Publication No. WO 95/20681.(A transcript image is a listing of the number of EST's for each of therepresented genes in a given tissue library. EST's sharing regions ofmutual sequence overlap are classified into clusters. A cluster isassigned a clone number from a representative 5′ EST. Often, a clusterof interest can be extended by comparing its consensus sequence withsequences of other EST's which did not meet the criteria for automatedclustering. The alignment of all available clusters and single EST'srepresent a contig from which a consensus sequence is derived.) Thetranscript images then were evaluated to identify EST sequences thatwere representative primarily of the breast tissue libraries. Thesetarget clones then were ranked according to their abundance (occurrence)in the target libraries and their absence from background libraries.Higher abundance clones with low background occurrence were given higherstudy priority. EST's corresponding to the BS249 consensus sequence,SEQUENCE ID NO 11 (or fragments thereof), were found in 40.7% (11 of 27)of breast tissue libraries. EST's corresponding to the BS249 consensussequence, SEQUENCE ID NO 11 (or fragments thereof), were found in only3.3% (16 of 476) of the other, non-breast libraries of the data base.Therefore, the consensus sequence or fragment thereof was found morethan 12 times more often in breast than non-breast tissues. Overlappingclones 3769673 (SEQUENCE ID NO 1), 2479915 (SEQUENCE ID NO 2), 2484355(SEQUENCE ID NO 3), 2823476 (SEQUENCE ID NO 4), 3618587 (SEQUENCE ID NO5), 2477279 (SEQUENCE ID NO 6), 640781 (SEQUENCE ID NO 7), 2476961(SEQUENCE ID NO 8), 3040836 (SEQUENCE ID NO 9) were identified forfurther study. These represented the minimum number of clones that(along with the full-length sequence of clone 3769673 [designated as3769673inh (SEQUENCE ID NO 10)] were needed to form the contig and fromwhich the consensus sequence provided herein (SEQUENCE ID NO 11) wasderived.

B. Generation of a Consensus Sequence. The nucleotide sequences ofclones 3769673 (SEQUENCE ID NO 1), 2479915 (SEQUENCE ID NO 2), 2484355(SEQUENCE ID NO 3), 2823476 (SEQUENCE ID NO 4), 3618587 (SEQUENCE ID NO5), 2477279 (SEQUENCE ID NO 6), 640781 (SEQUENCE ID NO 7), 2476961(SEQUENCE ID NO 8), 3040836 (SEQUENCE ID NO 9) and the full-lengthsequence of clone 3769673 [designated as 3769673inh (SEQUENCE ID NO 10)]were entered in the Sequencher™ Program (available from Gene CodesCorporation, Ann Arbor, Mich.) in order to generate a nucleotidealignment (contig map) and then generate their consensus sequence(SEQUENCE ID NO 11). FIGS. 1A-1D show the nucleotide sequence alignmentof these clones and their resultant nucleotide consensus sequence(SEQUENCE ID NO 11). FIG. 2 presents the contig map depicting the clones3769673 (SEQUENCE ID NO 1), 2479915 (SEQUENCE ID NO 2), 2484355(SEQUENCE ID NO 3), 2823476 (SEQUENCE ID NO 4), 3618587 (SEQUENCE ID NO5), 2477279 (SEQUENCE ID NO 6), 640781 (SEQUENCE ID NO 7), 2476961(SEQUENCE ID NO 8), 3040836 (SEQUENCE ID NO 9), and the full-lengthsequence of clone 3769673 [designated as 3769673inh (SEQUENCE ID NO 10)]which form overlapping regions of the BS249 gene and the resultantconsensus nucleotide sequence (SEQUENCE ID NO 11) of these clones in agraphic display. Following this, a three-frame translation was performedon the consensus sequence (SEQUENCE ID NO 11). The third forward framewas found to have an open reading frame encoding a 302 residue aminoacid sequence which is presented as SEQUENCE ID NO 23. The open readingframe corresponds to nucleotides 69 to 977 of SEQUENCE ID NO 11.

Example 2 Sequencing of BS249 EST-Specific Clones

DNA sequences for clones which comprise the most upstream and downstreamEST's of the BS249 gene contig were determined using dideoxy terminationsequencing with dye terminators following known methods [F. Sanger etal., Proc. Natl. Acad. Sci. USA 74:5463 (1977)].

Because vectors such as pSPORT1 (Life Technologies, Gaithersburg, Md.)and pINCY (available from Incyte Pharmaceuticals, Inc., Palo Alto,Calif.) contain universal priming sites just adjacent to the 3′ and 5′ligation junctions of the inserts, the inserts were sequenced in bothdirections using universal primers, SEQUENCE ID NO 14 and SEQUENCE ID NO15 (New England Biolabs, Beverly, Mass. and Applied Biosystems Inc,Foster City, Calif., respectively). The sequencing reactions were run ona polyacrylamide denaturing gel, and the sequences were determined by anApplied Biosystems 377 Sequencer (available from Applied Biosystems,Foster City, Calif.) or other sequencing apparatus. Additionalsequencing primers (SEQUENCE ID NOS 16-22) were designed from sequenceinformation of the consensus sequence (SEQUENCE ID NO 11). These primersthen were used to determine the remaining DNA sequence of the clonedinsert from each DNA strand, as previously described.

Example 3 Nucleic Acid

A. RNA Extraction from Tissue. Total RNA is isolated from breast tissuesand from non-breast tissues. Various methods are utilized, including butnot limited to the lithium chloride/urea technique, known in the art anddescribed by Kato et al., (J. Virol. 61:2182-2191, 1987), and TRIzol™(Gibco-BRL, Grand Island, N.Y.).

Briefly, tissue is placed in a sterile conical tube on ice and 10-15volumes of 3 M LiCl, 6 M urea, 5 mM EDTA, 0.1 M β-mercaptoethanol, 50 mMTris-HCl (pH 7.5) are added. The tissue is homogenized with a Polytron™homogenizer (Brinkman Instruments, Inc., Westbury, N.Y.) for 30-50 secon ice. The solution is transferred to a 15 ml plastic centrifuge tubeand placed overnight at −20° C. The tube is centrifuged for 90 min at9,000×g at 0-4° C. and the supernatant is immediately decanted. Ten mlof 3 M LiCl are added and the tube is vortexed for 5 sec. The tube iscentrifuged for 45 min at 11,000×g at 0-4° C. The decanting,resuspension in LiCl, and centrifugation is repeated and the finalpellet is air dried and suspended in 2 ml of 1 mM EDTA, 0.5% SDS, 10 mMTris (pH 7.5). Twenty microliters (20 μl) of Proteinase K (20 mg/ml) areadded, and the solution is incubated for 30 min at 37° C with occasionalmixing. One-tenth volume (0.22-0.25 ml) of 3 M NaCl is added and thesolution is vortexed before transfer into another tube containing 2 mlof phenol/chloroform/isoamyl alcohol (PCI). The tube is vortexed for 1-3sec and centrifuged for 20 min at 3,000×g at 10° C. The PCI extractionis repeated and followed by two similar extractions withchloroform/isoamyl alcohol (CI). The final aqueous solution istransferred to a prechilled 15 ml Corex glass tube containing 6 ml ofabsolute ethanol, the tube is covered with parafilm, and placed at −20°C. overnight. The tube is centrifuged for 30 min at 10,000×g at 0-4° C.and the ethanol supernatant is decanted immediately. The RNA pellet iswashed four times with 10 ml of 75% ice-cold ethanol and the finalpellet is air dried for 15 min at room temperature. The RNA is suspendedin 0.5 ml of 10 mM TE (pH 7.6, 1 mM EDTA) and its concentration isdetermined spectrophotometrically. RNA samples are aliquoted and storedat −70° C. as ethanol precipitates.

The quality of the RNA is determined by agarose gel electrophoresis (seeExample 5, Northern Blot Analysis) and staining with 0.5 μg/ml ethidiumbromide for one hour. RNA samples that do not contain intact rRNAs areexcluded from the study.

Alternatively, for RT-PCR analysis, 1 ml of Ultraspec RNA reagent isadded to 120 mg of pulverized tissue in a 2.0 ml polypropylene microfugetube, homogenized with a Polytron® homogenizer (Brinkman Instruments,Inc., Westbury, N.Y.) for 50 sec and placed on ice for 5 min. Then, 0.2ml of chloroform is added to each sample, followed by vortexing for 15sec. The sample is placed on ice for another 5 min, followed bycentrifugation at 12,000×g for 15 min at 4° C. The upper layer iscollected and transferred to another RNase-free 2.0 ml microfuge tube.An equal volume of isopropanol is added to each sample, and the solutionis placed on ice for 10 min. The sample is centrifuged at 12,000×g for10 min at 4° C., and the supernatant is discarded. The remaining pelletis washed twice with cold 75% ethanol, resuspended by vortexing, and theresuspended material is then pelleted by centrifugation at 7500×g for 5min at 4° C. Finally, the RNA pellet is dried in a Speedvac (Savant,Farmingdale, N.Y.) for 5 min and reconstituted in RNase-free water.

B. RNA Extraction from Blood Mononuclear Cells. Mononuclear cells areisolated from blood samples from patients by centrifugation usingFicoll-Hypaque as follows. A 10 ml volume of whole blood is mixed withan equal volume of RPMI Medium (Gibco-BRL, Grand Island, N.Y.). Thismixture is then underlayed with 10 ml of Ficoll-Hypaque (Pharmacia,Piscataway, N.J.) and centrifuged for 30 minutes at 200×g. The buffycoat containing the mononuclear cells is removed, diluted to 50 ml withDulbecco's PBS (Gibco-BRL, Grand Island, N.Y.) and the mixturecentrifuged for 10 minutes at 200×g. After two washes, the resultingpellet is resuspended in Dulbecco's PBS to a final volume of 1 ml.

RNA is prepared from the isolated mononuclear cells as described by N.Kato et al., J. Virology 61: 2182-2191 (1987). Briefly, the pelletedmononuclear cells are brought to a final volume of 1 ml and then areresuspended in 250 μL of PBS and mixed with 2.5 ml of 3M LiCl, 6M urea,5 mM EDTA, 0. 1M 2-mercaptoethanol, 50 mM Tris-HCl (pH 7.5). Theresulting mixture is homogenized and incubated at −20° C. overnight. Thehomogenate is centrifuged at 8,000 RPM in a Beckman J2-21M rotor for 90minutes at 0-4° C. The pellet is resuspended in 10 ml of 3M LiCl byvortexing and then centrifuged at 10,000 RPM in a Beckman J2-21M rotorcentrifuge for 45 minutes at 0-4° C. The resuspending and pelletingsteps then are repeated. The pellet is resuspended in 2 ml of 1 mM EDTA,0.5% SDS, 10 mM Tris (pH 7.5) and 400 μg Proteinase K with vortexing andthen it is incubated at 37° C. for 30 minutes with shaking. One tenthvolume of 3M NaCl then is added and the mixture is vortexed. Proteinsare removed by two cycles of extraction with phenol/chloroform/isoamylalcohol (PCI) followed by one extraction with chloroform/isoamyl alcohol(CI). RNA is precipitated by the addition of 6 ml of absolute ethanolfollowed by overnight incubation at −20° C. After the precipitated RNAis collected by centrifugation, the pellet is washed 4 times in 75%ethanol. The pelleted RNA is then dissolved in solution containing 1 nMEDTA, 10 mM Tris-HCl (pH 7.5).

Non-breast tissues are used as negative controls. The mRNA can befurther purified from total RNA by using commercially available kitssuch as oligo dT cellulose spin columns (Redicol™ from Pharmacia,Uppsala, Sweden) for the isolation of poly-adenylated RNA. Total RNA ormRNA can be dissolved in lysis buffer (5M guanidine thiocyanate, 0.1MEDTA, pH 7.0) for analysis in the ribonuclease protection assay.

C. RNA Extraction from polysomes. Tissue is minced in saline at 4° C.and mixed with 2.5 volumes of 0.8 M sucrose in a TK₁₅₀M (150 mM KCl, 5mM MgCl₂, 50 mM Tris-HCl, pH 7.4) solution containing 6 mM2-mercaptoethanol. The tissue is homogenized in a Teflon-glass Potterhomogenizer with five strokes at 100-200 rpm followed by six strokes ina Dounce homogenizer, as described by B. Mechler, Methods in Enzymology152:241-248 (1987). The homogenate then is centrifuged at 12,000×g for15 min at 4° C. to sediment the nuclei. The polysomes are isolated bymixing 2 ml of the supernatant with 6 ml of 2.5 M sucrose in TK₁₅₀M andlayering this mixture over 4 ml of 2.5 M sucrose in TK₁₅₀M in a 38 mlpolyallomer tube. Two additional sucrose TK₁₅₀M solutions aresuccessively layered onto the extract fraction; a first layer of 13 ml2.05 M sucrose followed by a second layer of 6 ml of 1.3 M sucrose. Thepolysomes are isolated by centrifuging the gradient at 90,000×g for 5 hrat 4° C. The fraction then is taken from the 1.3 M sucrose/2.05 Msucrose interface with a siliconized pasteur pipette and diluted in anequal volume of TE (10 mM Tris-HCl, pH 7.4, 1 mM EDTA). An equal volumeof 90° C. SDS buffer (1% SDS, 200 MM NaCl, 20 mM Tris-HCl, pH 7.4) isadded and the solution is incubated in a boiling water bath for 2 min.Proteins next are digested with a Proteinase K digestion (50 mg/ml) for15 min at 37° C. The mRNA is purified with 3 equal volumes ofphenol-chloroform extractions followed by precipitation with 0.1 volumeof 2 M sodium acetate (pH 5.2) and 2 volumes of 100% ethanol at −20° C.overnight. The precipitated RNA is recovered by centrifugation at12,000×g for 10 min at 4° C. The RNA is dried and resuspended in TE (pH7.4) or distilled water. The resuspended RNA then can be used in a slotblot or dot blot hybridization assay to check for the presence of BS249mRNA (see Example 6).

The quality of nucleic acid and proteins is dependent on the method ofpreparation used. Each sample may require a different preparationtechnique to maximize isolation efficiency of the target molecule. Thesepreparation techniques are within the skill of the ordinary artisan.

Example 4 Ribonuclease Protection Assay

A. Synthesis of Labeled Complementary RNA (cRNA) Hybridization Probe andUnlabeled Sense Strand. Labeled antisense and unlabeled sense riboprobesare transcribed from the BS249 gene cDNA sequence which contains a 5′RNA polymerase promoter such as SP6 or T7. The sequence may be from avector containing the appropriate BS249 cDNA insert, or from aPCR-generated product of the insert using PCR primers which incorporatea 5′ RNA polymerase promoter sequence. For example, the describedplasmid, clone 98679 or another comparable clone, containing the BS249gene cDNA sequence, flanked by opposed SP6 and T7 or other RNApolymerase promoters, is purified using a Qiagen Plasmid PurificationKit (Qiagen, Chatsworth, Calif.). Then 10 μg of the plasmid DNA arelinearized by cutting with an appropriate restriction enzyme such as DdeI for 1 hr at 37° C. The linearized plasmid DNA is purified using theQIAprep Kit (Qiagen, Chatsworth, Calif.) and used for the synthesis ofantisense transcript from the appropriate promoter using the Riboprobe®in vitro Transcription System (Promega Corporation, Madison, Wis.), asdescribed by the supplier's instructions, incorporating either(alpha³²P) CTP (Amersham Life Sciences, Inc. Arlington Heights, Ill.) orbiotinylated CTP as a label. To generate the sense strand, 10 μg of thepurified plasmid DNA are cut with restriction enzymes, such as Xba I andNot I, and transcribed as above from the appropriate promoter. Bothsense and antisense strands are isolated by spin column chromatography.Unlabeled sense strand is quantitated by UV absorption at 260 nm.

B. Hybridization of Labeled Probe to Target. Frozen tissue is pulverizedto powder under liquid nitrogen and 100-500 mg are dissolved in 1 ml oflysis buffer, available as a component of the Direct Protect™ LysateRNase Protection Kit (Ambion, Inc., Austin, Tex.). Further dissolutioncan be achieved using a tissue homogenizer. In addition, a dilutionseries of a known amount of sense strand in mouse liver lysate is madefor use as a positive control. Finally, 45 μl of solubilized tissue ordiluted sense strand is mixed directly with either; 1) 1×10⁵ cpm ofradioactively labeled probe, or 2) 250 pg of non-isotopically labeledprobe in 5 μl of lysis buffer. Hybridization is allowed to proceedovernight at 37° C. See, T. Kaabache et al., Anal. Biochem. 232:225-230(1995).

C. RNase Digestion. RNA that is not hybridized to probe is removed fromthe reaction as per the Direct Protect™ protocol using a solution ofRNase A and RNase T1 for 30 min at 37° C., followed by removal of RNaseby Proteinase K digestion in the presence of sodium sarcosyl. Hybridizedfragments protected from digestion are then precipitated by the additionof an equal volume of isopropanol and placed at −70° C. for 3 hr. Theprecipitates are collected by centrifugation at 12,000×g for 20 min.

D. Fragment Analysis. The precipitates are dissolved in denaturing gelloading dye (80% formamide, 10 mM EDTA (pH 8.0), 1 mg/ml xylene cyanol,1 mg/ml bromophenol blue), heat denatured, and electrophoresed in 6%polyacrylamide TBE, 8 M urea denaturing gels. The gels are imaged andanalyzed using the STORM™ storage phosphor autoradiography system(Molecular Dynamics, Sunnyvale, Calif.). Quantitation of protectedfragment bands, expressed in femtograms (fg), is achieved by comparingthe peak areas obtained from the test samples to those from the knowndilutions of the positive control sense strand (see Section B, supra).The results are expressed in molecules of BS249 RNA/cell and as a imagerating score. In cases where non-isotopic labels are used, hybrids aretransferred from the gels to membranes (nylon or nitrocellulose) byblotting and then analyzed using detection systems that employstreptavidin alkaline phosphatase conjugates and chemiluminesence orchemifluoresence reagents.

Detection of a product comprising a sequence selected from the groupconsisting of SEQUENCE ID NOS 1-11, and fragments or complementsthereof, is indicative of the presence of BS249 mRNA(s), suggesting adiagnosis of a breast tissue disease or condition, such as breastcancer.

Example 5 Northern Blotting

The Northern blot technique is used to identify a specific size RNAfragment from a complex population of RNA using gel electrophoresis andnucleic acid hybridization. Northern blotting is well-known technique inthe art. Briefly, 5-10 μg of total RNA (see Example 3) are incubated in15 μl of a solution containing 40 mM morphilinopropanesulfonic acid(MOPS) (pH 7.0), 10 mM sodium acetate, 1 mM EDTA, 2.2 M formaldehyde,50% v/v formamide for 15 min at 65° C. The denatured RNA is mixed with 2μl of loading buffer (50% glycerol, 1 mM EDTA, 0.4% bromophenol blue,0.4% xylene cyanol) and loaded into a denaturing 1.0% agarose gelcontaining 40 mM MOPS (pH 7.0), 10 mM sodium acetate, 1 mM EDTA and 2.2M formaldehyde. The gel is electrophoresed at 60 V for 1.5 hr and rinsedin RNAse free water. RNA is transferred from the gel onto nylonmembranes (Brightstar-Plus, Ambion, Inc., Austin, Tex.) for 1.5 hoursusing the downward alkaline capillary transfer method (Chomczynski,Anal. Biochem. 201:134-139, 1992). The filter is rinsed with 1×SSC, andRNA is crosslinked to the filter using a Stratalinker™ (Stratagene,Inc., La Jolla, Calif.) on the autocrosslinking mode and dried for 15min. The membrane is then placed into a hybridization tube containing 20ml of preheated prehybridization solution (5×SSC, 50% formamide,5×Denhardt's solution, 100 μg/ml denatured salmon sperm DNA) andincubated in a 42° C. hybridization oven for at least 3 hr. While theblot is prehybridizing, a ³²P-labeled random-primed probe is generatedusing the BS249 insert fragment (obtained by digesting clone 98679 oranother comparable clone with XbaI and NotI) using Random Primer DNALabeling System (Life Technologies, Inc., Gaithersburg, Md.) accordingto the manufacturer's instructions. Half of the probe is boiled for 10min, quick chilled on ice and added to the hybridization tube.Hybridization is carried out at 42° C. for at least 12 hr. Thehybridization solution is discarded and the filter is washed in 30 ml of3×SSC, 0.1% SDS at 42° C. for 15 min, followed by 30 ml of 3×SSC, 0.1%SDS at 42° C. for 15 min. The filter is wrapped in Saran Wrap, exposedto Kodak XAR-Omat film for 8-96 hr, and the film is developed foranalysis. High level of expression of mRNA corresponding to a sequenceselected from the group consisting of SEQUENCE ID NOS 1-11, andfragments or complements thereof, is an indication of the presence ofBS249 mRNA, suggesting a diagnosis of a breast tissue disease orcondition, such as breast cancer.

Example 6 Dot Blot/Slot Blot

Dot and slot blot assays are quick methods to evaluate the presence of aspecific nucleic acid sequence in a complex mix of nucleic acid. Toperform such assays, up to 50 μg of RNA are mixed in 50 μl of 50%formamide, 7% formaldehyde, 1×SSC, incubated 15 min at 68° C., and thencooled on ice. Then, 100 μl of 20×SSC are added to the RNA mixture andloaded under vacuum onto a manifold apparatus that has a preparednitrocellulose or nylon membrane. The membrane is soaked in water,20×SSC for 1 hour, placed on two sheets of 20×SSC prewet Whatman #3filter paper, and loaded into a slot blot or dot blot vacuum manifoldapparatus. The slot blot is analyzed with probes prepared and labeled asdescribed in Example 4, supra. Detection of mRNA corresponding to asequence selected from the group consisting of SEQUENCE ID NOS 1-11, andfragments or complements thereof, is an indication of the presence ofBS249, suggesting a diagnosis of a breast tissue disease or condition,such as breast cancer.

Other methods and buffers which can be utilized in the methods describedin Examples 5 and 6, but not specifically detailed herein, are known inthe art and are described in J. Sambrook et al., supra which isincorporated herein by reference.

Example 7 In Situ Hybridization

This method is useful to directly detect specific target nucleic acidsequences in cells using detectable nucleic acid hybridization probes.

Tissues are prepared with cross-linking fixative agents such asparaformaldehyde or glutaraldehyde for maximum cellular RNA retention.See, L. Angerer et al., Methods in Cell Biol. 35:37-71 (1991). Briefly,the tissue is placed in greater than 5 volumes of 1% glutaraldehyde in50 mM sodium phosphate, pH 7.5 at 4° C. for 30 min. The solution ischanged with fresh glutaraldehyde solution (1% glutaraldehyde in 50 mMsodium phosphate, pH 7.5) for a further 30 min fixing. The fixingsolution should have an osmolality of approximately 0.375% NaCl. Thetissue is washed once in isotonic NaCl to remove the phosphate.

The fixed tissues then are embedded in paraffin as follows. The tissueis dehydrated though a series of increasing ethanol concentrations for15 min each: 50% (twice), 70% (twice), 85%, 90% and then 100% (twice).Next, the tissue is soaked in two changes of xylene for 20 min each atroom temperature. The tissue is then soaked in two changes of a 1:1mixture of xylene and paraffin for 20 min each at 60° C.; and then inthree final changes of paraffin for 15 min each.

Next, the tissue is cut in 5 μm sections using a standard microtome andplaced on a slide previously treated with a tissue adhesive such as3-aminopropyltriethoxysilane.

Paraffin is removed from the tissue by two 10 min xylene soaks andrehydrated in a series of decreasing ethanol concentrations: 99% twice,95%, 85%, 70%, 50%, 30%, and then distilled water twice. The sectionsare pre-treated with 0.2 M HCl for 10 min and permeabilized with 2 μg/mlProteinase K at 37° C. for 15 min.

Labeled riboprobes transcribed from the BS249 gene plasmid (see Example4) are hybridized to the prepared tissue sections and incubatedovernight at 56° C. in 3× standard saline extract and 50% formamide.Excess probe is removed by washing in 2× standard saline citrate and 50%formamide followed by digestion with 100 μg/ml RNase A at 37° C. for 30min. Fluorescence probe is visualized by illumination with ultraviolet(UV) light under a microscope. Fluorescence in the cytoplasm isindicative of BS249 mRNA. Alternatively, the sections can be visualizedby autoradiography.

Example 8 Reverse Transcription PCR

A. One Step RT-PCR Assay. Target-specific primers are designed to detectthe above-described target sequences by reverse transcription PCR usingmethods known in the art. One step RT-PCR is a sequential procedure thatperforms both RT and PCR in a single reaction mixture. The procedure isperformed in a 200 μl reaction mixture containing 50 mM(N,N,-bis[2-Hydroxyethyl]glycine), pH 8.15, 81.7 mM KOAc, 33.33 mM KOH,0.01 mg/ml bovine serum albumin, 0.1 mM ethylene diaminetetraaceticacid, 0.02 mg/ml NaN₃, 8% w/v glycerol, 150 μM each of dNTP, 0.25 μMeach primer, 5U rTth polymerase, 3.25 mM Mn(OAc)₂ and 5 μl of target RNA(see Example 3). Since RNA and the rTth polymerase enzyme are unstablein the presence of Mn(OAc)₂, the Mn(OAc)₂ should be added just beforetarget addition. Optimal conditions for cDNA synthesis and thermalcycling readily can be determined by those skilled in the art. Thereaction is incubated in a Perkin-Elmer Thermal Cycler 480. Conditionswhich may be found useful include cDNA synthesis at 60°-70° C. for 15-45min and 30-45 amplification cycles at 94° C., 1 min; 55°-70° C., 1 min;min. One step RT-PCR also may be performed by using a dual enzymeprocedure with Taq polymerase and a reverse transcriptase enzyme, suchas MMLV (Moloney murine leukemia virus) or AMV (avian myeloblastosisvirus) RT (reverse transcriptase) enzymes.

B. Traditional RT-PCR. Alternatively, a traditional two-step RT-PCRreaction may be performed, as described by K. Q. Hu et al., Virology181:721-726 (1991), as follows. The extracted mRNA is transcribed in a25 μL reaction mixture containing 10 mM Tris-HCl, pH 8.3, 5 mM MgCl2,500 μM dNTP, 20 U RNasin, 1 μM antisense primer and 25 U AMV or MMLVreverse transcriptase. Reverse transcription is performed at 37-45° C.for 30-60 min, followed by further incubation at 95° C. for 5 min toinactivate the RT. PCR is performed using 10 μl of the cDNA reaction ina final PCR reaction volume of 50 μl containing 10 mM Tris-HCl (pH 8.3),50 mM KCl, 2 mM MgCl₂, 200 μM dNTP, 0.5 μM of each primer and 2.5 U ofTaq polymerase. Optimal conditions for cDNA synthesis and thermalcycling can be readily determined by those skilled in the art. Thereaction is incubated in a Perkin-Elmer Thermal Cycler 480 or othercomparable instrument. Conditions which may be found useful include30-45 cycles of amplification (94° C., 1 min; 55-70° C., 1 min; 72° C.,2 min), final extension (72° C., 10 min) and soak at 4° C.

C. PCR Fragment Analysis. The correct products then can be verified bysize determination using gel electrophoresis with SYBR® Green I nucleicacid gel stain (Molecular Probes, Eugene, Oreg.) and imaged using aSTORM imaging system, or also verified by Southern, dot or slot blotanalysis using a labeled probe against the internal sequences of the PCRproduct. The probes also may be polynucleotides analogs, such asmorpholinos or peptide nucleic acids analogs (PNAs). Detection of aproduct comprising a sequence selected from the group consisting ofSEQUENCE ID NOS 1-11, and fragments or complements thereof, isindicative of the presence of BS249 mRNA(s), suggesting a diagnosis of abreast tissue disease or condition, such as breast cancer.

Example 9 OH-PCR

A. Probe selection and Labeling. Target-specific primers and probes aredesigned to detect the above-described target sequences byoligonucleotide hybridization PCR. International Publication Nos WO92/10505, published Jun. 25, 1992, and WO 92/11388, published Jul. 9,1992, teach methods for labeling oligonucleotides at their 5′ and 3′ends, respectively. According to one known method for labeling anoligonucleotide, a label-phosphoramidite reagent is prepared and used toadd the label to the oligonucleotide during its synthesis. For example,see N. T. Thuong et al., Tet. Letters 29(46):5905-5908 (1988); or J. S.Cohen et al., published U.S. patent application Ser. No. 07/246,688(NTIS ORDER No. PAT-APPL-7-246,688) (1989). Preferably, probes arelabeled at their 3′ end to prevent participation in PCR and theformation of undesired extension products. For one step OH-PCR, theprobe should have a T_(M) at least 15° C. below the T_(M) of theprimers. The primers and probes are utilized as specific bindingmembers, with or without detectable labels, using standardphosphoramidite chemistry and/or post-synthetic labeling methods whichare well-known to one skilled in the art.

B. One Step Oligo Hybridization PCR. OH-PCR is performed on a 200 μlreaction containing 50 mM (N,N,-bis[2-Hydroxyethyl]glycine), pH 8.15,81.7 mM KOAc, 33.33 mM KOH, 0.01 mg/ml bovine serum albumin, 0.1 mMethylene diaminetetraacetic acid, 0.02 mg/ml NaN₃, 8% w/v glycerol, 150μM each of dNTP, 0.25 μM each primer, 3.75 nM probe, 5U rTth polymerase,3.25 mM Mn(OAc)₂ and 5 μl blood equivalents of target (see Example 3).Since RNA and the rTth polymerase enzyme are unstable in the presence ofMn(OAc)₂, the Mn(OAc)₂ should be added just before target addition. Thereaction is incubated in a Perkin-Elmer Thermal Cycler 480. Optimalconditions for cDNA synthesis and thermal cycling can be readilydetermined by those skilled in the art. Conditions which may be founduseful include cDNA synthesis (60° C., 30 min), 30-45 amplificationcycles (94° C., 40 sec; 55-70° C., 60 sec), oligo-hybridization (97° C.,5 min; 15° C., 5 min; 15° C. soak). The correct reaction productcontains at least one of the strands of the PCR product and aninternally hybridized probe.

C. OH-PCR Product Analysis. Amplified reaction products are detected onan LCx® Analyzer system (available from Abbott Laboratories, AbbottPark, Ill.). Briefly, the correct reaction product is captured by anantibody labeled microparticle at a capturable site on either the PCRproduct strand or the hybridization probe, and the complex is detectedby binding of a detectable antibody conjugate to either a detectablesite on the probe or the PCR strand. Only a complex containing a PCRstrand hybridized with the internal probe is detectable. The detectionof this complex then is indicative of the presence of BS249 mRNA,suggesting a diagnosis of a breast disease or condition, such as breastcancer.

Many other detection formats exist which can be used and/or modified bythose skilled in the art to detect the presence of amplified ornon-amplified BS249-derived nucleic acid sequences including, but notlimited to, ligase chain reaction (LCR, Abbott Laboratories, AbbottPark, Ill.); Q-beta replicase (Gene-TrakTm, Naperville, Ill.), branchedchain reaction (Chiron, Emeryville, Calif.) and strand displacementassays (Becton Dickinson, Research Triangle Park, N.C.).

Example 10 Synthetic Peptide Production

Synthetic peptides were modeled and then prepared based upon thepredicted amino acid sequence of the BS249 polypeptide consensussequence (see Example 1). In particular, a number of BS249 peptidesderived from SEQUENCE ID NO 23 were prepared, including the peptides ofSEQUENCE ID NO 24, SEQUENCE ID NO 25, SEQUENCE ID NO 26 and SEQUENCE IDNO 27. All peptides were synthesized on a Symphony Peptide Synthesizer(available from Rainin Instrument Co, Emeryville, Calif.) using FMOCchemistry, standard cycles and in-situ HBTU activation. Cleavage anddeprotection conditions were as follows: a volume of 2.5 ml of cleavagereagent (77.5% v/v trifluoroacetic acid, 15% v/v ethanedithiol, 2.5% v/vwater, 5% v/v thioanisole, 1-2% w/v phenol) were added to the resin, andagitated at room temperature for 2-4 hours. The filtrate was thenremoved and the peptide was precipitated from the cleavage reagent withcold diethyl ether. Each peptide was filtered, purified viareverse-phase preparative HPLC using a water/acetonitrile/0.1% TFAgradient, and lyophilized. The product was confirmed by massspectrometry (see Example 12).

Example 11a Expression of Protein in a Cell Line Using Plasmid 577

A. Construction of a BS249 Expression Plasmid. Plasmid 577, described inU.S. patent application Ser. No. 08/478,073, filed Jun. 7, 1995 andincorporated herein by reference, has been constructed for theexpression of secreted antigens in a permanent cell line. This plasmidcontains the following DNA segments: (a) a 2.3 kb fragment of pBR322containing bacterial beta-lactamase and origin of DNA replication; (b) a1.8 kb cassette directing expression of a neomycin resistance gene undercontrol of HSV-1 thymidine kinase promoter and poly-A addition signals;(c) a 1.9 kb cassette directing expression of a dihydrofolate reductasegene under the control of an Simian Virus 40 (SV40) promoter and poly-Aaddition signals; (d) a 3.5 kb cassette directing expression of a rabbitimmunoglobulin heavy chain signal sequence fused to a modified hepatitisC virus (HCV) E2 protein under the control of the Simian Virus 40 T-Agpromoter and transcription enhancer, the hepatitis B virus surfaceantigen (HBsAg) enhancer I followed by a fragment of Herpes SimplexVirus-1 (HSV-1) genome providing poly-A addition signals; and (e) aresidual 0.7 kb fragment of SV40 genome late region of no function inthis plasmid. All of the segments of the vector were assembled bystandard methods known to those skilled in the art of molecular biology.

Plasmids for the expression of secretable BS249 proteins are constructedby replacing the hepatitis C virus E2 protein coding sequence in plasmid577 with that of a BS249 polynucleotide sequence selected from the groupconsisting of SEQUENCE ID NOS 1-11 and fragments or complements thereof,as follows. Digestion of plasmid 577 with XbaI releases the hepatitis Cvirus E2 gene fragment. The resulting plasmid backbone allows insertionof the BS249 cDNA insert downstream of the rabbit immunoglobulin heavychain signal sequence which directs the expressed proteins into thesecretory pathway of the cell. The BS249 cDNA fragment is generated byPCR using standard procedures. Encoded in the sense PCR primer sequenceis an XbaI site, immediately followed by a 12 nucleotide sequence thatencodes the amino acid sequence Ser-Asn-Glu-Leu (“SNEL”) to promotesignal protease processing, efficient secretion and final productstability in culture fluids. Immediately following this 12 nucleotidesequence the primer contains nucleotides complementary to templatesequences encoding amino acids of the BS249 gene. The antisense primerincorporates a sequence encoding the following eight amino acids justbefore the stop codons: Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys (SEQUENCE ID NO28). Within this sequence is incorporated a recognition site to aid inanalysis and purification of the BS249 protein product. A recognitionsite (termed “FLAG”) that is recognized by a commercially availablemonoclonal antibody designated anti-FLAG M2 (Eastman Kodak, Co., NewHaven, Conn.) can be utilized, as well as other comparable sequences andtheir corresponding antibodies. For example, PCR is performed usingGeneAmp® reagents obtained from Perkin-Elmer-Cetus, as directed by thesupplier's instructions. PCR primers are used at a final concentrationof 0.5 μM. PCR is performed on the BS249 plasmid template in a 100 μlreaction for 35 cycles (94° C., 30 seconds; 55° C., 30 seconds; 72° C.,90 seconds) followed by an extension cycle of 72° C. for 10 min.

B. Transfection of Dihydrofolate Reductase Deficient Chinese HamsterOvary Cells. The plasmid described supra is transfected intoCHO/dhfr-cells [DXB-111, Uriacio et al., Proc. Natl. Acad. Sci. USA77:4451-4466 (1980)]. These cells are available from the A.T.C.C., 12301Parklawn Drive, Rockville, Md. 20852, under Accession No. CRL 9096.Transfection is carried out using the cationic liposome-mediatedprocedure described by P. L. Felgner et al., Proc. Natl. Acad. Sci. USA84:7413-7417 (1987). Particularly, CHO/dhfr- cells are cultured in Ham'sF-12 media supplemented with 10% fetal calf serum, L-glutamine (1 mM)and freshly seeded into a flask at a density of 5-8×10⁵ cells per flask.The cells are grown to a confluency of between 60 and 80% fortransfection. Twenty micrograms (20 μg) of plasmid DNA are added to 1.5ml of Opti-MEM I medium and 100 μl of Lipofectin Reagent (Gibco-BRL;Grand Island, N.Y.) are added to a second 1.5 ml portion of Opti-MEM Imedia. The two solutions are mixed and incubated at room temperature for20 min. After the culture medium is removed from the cells, the cellsare rinsed 3 times with 5 ml of Opti-MEM I medium. The Opti-MEMI-Lipofection-plasmid DNA solution then is overlaid onto the cells. Thecells are incubated for 3 hr at 37° C., after which time the Opti-MEMI-Lipofectin-DNA solution is replaced with culture medium for anadditional 24 hr prior to selection.

C. Selection and Amplification. One day after transfection, cells arepassaged 1:3 and incubated with dhfr/G418 selection medium (hereafter,“F-12 minus medium G”). Selection medium is Ham's F-12 with L-glutamineand without hypoxanthine, thymidine and glycine (JRH Biosciences,Lenexa, Kans.) and 300 μg per ml G418 (Gibco-BRL; Grand Island, N.Y.).Media volume-to-surface area ratios of 5 ml per 25 cm² are maintained.After approximately two weeks, DHFR/G418 cells are expanded to allowpassage and continuous maintenance in F-12 minus medium G.

Amplification of each of the transfected BS249 cDNA sequences isachieved by stepwise selection of DHFR⁺, G418⁺ cells with methotrexate(reviewed by R. Schimke, Cell 37:705-713 [1984]). Cells are incubatedwith F-12 minus medium G containing 150 nM methotrexate (MTX) (Sigma,St. Louis, Mo.) for approximately two weeks until resistant coloniesappear. Further gene amplification is achieved by selection of 150 nMadapted cells with 5 μM MTX.

D. Antigen Production. F-12 minus medium G supplemented with 5 μM MTX isoverlaid onto just confluent monolayers for 12 to 24 hr at 37° C. in 5%CO₂. The growth medium is removed and the cells are rinsed 3 times withDulbecco's phosphate buffered saline (PBS) (with calcium and magnesium)(Gibco-BRL; Grand Island, N.Y.) to remove the remaining media/serumwhich may be present. Cells then are incubated with VAS custom medium(VAS custom formulation with L-glutamine with HEPES without phenol red,available from JRH Bioscience; Lenexa, Kans., product number 52-08678P),for 1 hr at 37° C. in 5% CO₂. Cells then are overlaid with VAS forproduction at 5 ml per T flask. Medium is removed after seven days ofincubation, retained, and then frozen to await purification withharvests 2, 3 and 4. The monolayers are overlaid with VAS for 3 moreseven day harvests.

E. Analysis of Breast Tissue Gene BS249 Antigen Expression. Aliquots ofVAS supernatants from the cells expressing the BS249 protein constructare analyzed, either by SDS-polyacrylamide gel electrophoresis(SDS-PAGE) using standard methods and reagents known in the art(Laemnili discontinuous gels), or by mass spectrometry.

F. Purification. Purification of the BS249 protein containing the FLAGsequence is performed by immunoaffinity chromatography using an affinitymatrix comprising anti-FLAG M2 monoclonal antibody covalently attachedto agarose by hydrazide linkage (Eastman Kodak Co., New Haven, Conn.).Prior to affinity purification, protein in pooled VAS medium harvestsfrom roller bottles is exchanged into 50 mM Tris-HCl (pH 7.5), 150 mMNaCl buffer using a Sephadex G-25 (Pharmacia Biotech Inc., Uppsala,Sweden) column. Protein in this buffer is applied to the anti-FLAG M2antibody affinity column. Non-binding protein is eluted by washing thecolumn with 50 mM Tris-HCl (pH 7.5), 150 mM NaCl buffer. Bound proteinis eluted using an excess of FLAG peptide in 50 mM Tris-HCl (pH 7.5),150 mM NaCl. The excess FLAG peptide can be removed from the purifiedBS249 protein by gel electrophoresis or HPLC.

Although plasmid 577 is utilized in this example, it is known to thoseskilled in the art that other comparable expression systems, such asCMV, can be utilized herein with appropriate modifications in reagentand/or techniques and are within the skill of the ordinary artisan.

The largest cloned insert containing the coding region of the BS249 geneis then sub-cloned into either (i) a eukaryotic expression vector whichmay contain, for example, a cytomegalovirus (CMV) promoter and/orprotein fusible sequences which aid in protein expression and detection,or (ii) a bacterial expression vector containing a superoxide-dismutase(SOD) and CMP-KDO synthetase (CKS) or other protein fusion gene forexpression of the protein sequence. Methods and vectors which are usefulfor the production of polypeptides which contain fusion sequences of SODare described in EPO 0196056, published Oct. 1, 1986, which isincorporated herein by reference and those containing fusion sequencesof CKS are described in EPO Publication No. 0331961, published Sep. 13,1989, which publication is also incorporated herein by reference. Thisso-purified protein can be used in a variety of techniques, including,but not limited to animal immunization studies, solid phaseimmunoassays, etc.

Example 11b Expression of Protein in a Cell Line Using pcDNA3.1/Myc-His

A. Construction of a BS249 Expression Plasmid. Plasmid pcDNA3.1/Myc-His(Cat.# V855-20, Invitrogen, Carlsbad, Calif.) has been constructed, inthe past, for the expression of secreted antigens by most mammalian celllines. Expressed protein inserts are fused to a myc-his peptide tag. Themyc-his tag (SEQUENCE ID NO 29) comprises a c-myc oncoprotein epitopeand a polyhistidine sequence which are useful for the purification of anexpressed fusion protein by using either anti-myc or anti-his affinitycolumns, or metalloprotein binding columns.

Plasmids for the expression of secretable BS249 proteins are constructedby inserting a BS249 polynucleotide sequence selected from the groupconsisting of SEQUENCE ID NOS 1-11, and fragments or complementsthereof. Prior to construction of a BS249 expression plasmid, the BS249cDNA sequence is first cloned into a pCR®-Blunt vector as follows:

The BS249 cDNA fragment is generated by PCR using standard procedures.For example, PCR is performed procedures and reagents from Stratagene®,Inc. (La Jolla, Calif.), as directed by the manufacturer. PCR primersare used at a final concentration of 0.5 μM. PCR using 5 U of pfupolymerase (Stratagene, La Jolla, Calif.) is performed on the BS249plasmid template (see Example 2) in a 50 μl reaction for 30 cycles (94°C., 1 min; 65° C., 1.5 min; 72° C, 3 min) followed by an extension cycleof 72° C. for 8 min. (The sense PCR primer sequence comprisesnucleotides which are either complementary to the pINCY vector directlyupstream of the BS249 gene insert or which incorporate a 5′ EcoRIrestriction site, an adjacent downstream protein translation consensusinitiator, and a 3′ nucleic acid sequence which is the same sense as the5′-most end of the BS249 cDNA insert. The antisense PCR primerincorporates a 5′ NotI restriction sequence and a sequence complementaryto the 3′ end of the BS249 cDNA insert just upstream of the 3′-most,in-frame stop codon.) Five microliters (5 μl) of the resultingblunted-ended PCR product are ligated into 25 ng of linearizedpCR®-Blunt vector (Invitrogen, Carlsbad, Calif.) interrupting the lethalccdB gene of the vector. The resulting ligated vector is transformedinto TOP10 E. coli (Invitrogen, Carlsbad, Calif.) using a One ShotsTransformation Kit (Invitrogen, Carlsbad, Calif.) followingmanufacturer's instructions. The transformed cells are grown on LB-Kan(50 μg/ml kanamycin) selection plates at 37° C. Only cells containing aplasmid with an interrupted ccdB gene will grow after transformation[Grant, S. G. N., Proc. Natl. Acad. Sci. USA 87:4645-4649 (1990)].Transformed colonies are picked and grown up in 3 ml of LB-Kan broth at37° C. Plasmid DNA is isolated by using a QIAprep® (Qiagen Inc., SantaClarita, Calif.) procedure, as directed by the manufacturer. The DNA iscut with EcoRI or SnaBI, and NotI restriction enzymes to release theBS249 insert fragment. The fragment is run on 1% Seakem® LE agarose/0.5μg/ml ethidium bromide/TE gel, visualized by UV irradiation, excised andpurified using QIAquick™ (Qiagen Inc., Santa Clarita, Calif.)procedures, as directed by the supplier's instructions.

The pcDNA3.1/Myc-His plasmid DNA is linearized by digestion with EcoRIor SnaBI, and NotI in the polylinker region of the plasmid DNA. Theresulting plasmid DNA backbone allows insertion of the BS249 purifiedcDNA fragment, supra, downstream of a CMV promoter which directsexpression of the proteins in mammalian cells. The ligated plasmid istransformed into DH5 alpha™ cells (GibcoBRL Grand Island, N.Y.), asdirected by the manufacturer. Briefly, 10 ng of pcDNA3.1/Myc-Hiscontaining a BS249 insert are added to 50 μl of competent DH5 alphacells, and the contents are mixed gently. The mixture is incubated onice for 30 min, heat shocked for 20 sec at 37° C., and placed on ice foran additional 2 min. Upon addition of 0.95 ml of LB medium, the mixtureis incubated for 1 hr at 37° C. while shaking at 225 rpm. Thetransformed cells then are plated onto 100 mm LB/Amp (50 μg/mlampicillin) plates and grown at 37° C. Colonies are picked and grown in3 ml of LB/Amp broth. Plasmid DNA is purified using a QIAprep Kit. Thepresence of the insert is confirmed using techniques known to thoseskilled in the art, including, but not limited to restriction digestionand gel analysis. (J. Sambrook et al., supra.)

B. Transfection of Human Embryonic Kidney Cell 293 Cells. The BS249expression plasmid described in section A, supra, is retransformed intoDH5 alpha cells, plated onto LB/ampicillin agar, and grown up in 10 mlof LB/ampicillin broth, as described hereinabove. The plasmid ispurified using a QIAfilter™ Maxi Kit (Qiagen, Chatsworth, Calif.) and istransfected into HEK293 cells [F. L. Graham et al., J. Gen. Vir.36:59-72 (1977)]. These cells are available from the A.T.C.C, 10801University Blvd. Manassas, Va., 20110 under Accession No. CRL 1573.Transfection is carried out using the cationic lipofectamine-mediatedprocedure described by P. Hawley-Nelson et al., Focus 15.73 (1993).Particularly, HEK293 cells are cultured in 10 ml DMEM media supplementedwith 10% fetal bovine serum (FBS), L-glutamine (2 mM) and freshly seededinto 100 mm culture plates at a density of 9×10⁶ cells per plate. Thecells are grown at 37° C. to a confluency of between 70% and 80% fortransfection. Eight micrograms (8 μg) of plasmid DNA are added to 800 μlof Opti-MEM I® medium (Gibco-BRL, Grand Island, N.Y.), and 48-96 μl ofLipofectamine™ Reagent (Gibco-BRL, Grand Island, N.Y.) are added to asecond 800 μl portion of Opti-MEM I media. The two solutions are mixedand incubated at room temperature for 15-30 min. After the culturemedium is removed from the cells, the cells are washed once with 10 mlof serum-free DMEM. The Opti-MEM I-Lipofectamine-plasmid DNA solution isdiluted with 6.4 ml of serum-free DMEM and then overlaid onto the cells.The cells are incubated for 5 hr at 37° C., after which time, anadditional 8 ml of DMEM with 20% FBS are added. After 18-24 hr, the oldmedium is aspirated, and the cells are overlaid with 5 ml of fresh DMEMwith 5% FBS. Supernatants and cell extracts are analyzed for BS249 geneactivity 72 hr after transfection.

C. Analysis of Breast Tissue Gene BS249 Antigen Expression. The culturesupernatant, supra, is transferred to cryotubes and stored on ice.HEK293 cells are harvested by washing twice with 10 ml of coldDulbecco's PBS and lysing by addition of 1.5 ml of CAT lysis buffer(Boehringer Mannheim, Indianapolis, Ind.), followed by incubation for 30min at room temperature. Lysate is transferred to 1.7 ml polypropylenemicrofuge tubes and centrifuged at 1000×g for 10 min. The supernatant istransferred to new cryotubes and stored on ice. Aliquots of supernatantsfrom the cells and the lysate of the cells expressing the BS249 proteinconstruct are analyzed for the presence of BS249 recombinant protein.The aliquots can be run on SDS-polyacrylamide gel electrophoresis(SDS-PAGE) using standard methods and reagents known in the art. (J.Sambrook et al., supra) These gels can then be blotted onto a solidmedium such as nitrocellulose, nytran, etc., and the BS249 protein bandcan be visualized using Western blotting techniques with anti-mycepitope or anti-histidine monoclonal antibodies (Invitrogen, Carlsbad,Calif.) or anti-BS249 polyclonal serum (see Example 14). Alternatively,the expressed BS249 recombinant protein can be analyzed by massspectrometry (see Example 12).

D. Purification. Purification of the BS249 recombinant proteincontaining the myc-his sequence is performed using the Xpress® affinitychromatography system (Invitrogen, Carlsbad, Calif.) containing anickel-charged agarose resin which specifically binds polyhistidineresidues. Supernatants from 10 x 100 mm plates, prepared as describedsupra, are pooled and passed over the nickel-charged column. Non-bindingprotein is eluted by washing the column with 50 mM Tris-HCl (pH 7.5)/150mM NaCl buffer, leaving only the myc-his fusion proteins. Bound BS249recombinant protein then is eluted from the column using either anexcess of imidazole or histidine, or a low pH buffer. Alternatively, therecombinant protein can also be purified by binding at the myc-hissequence to an affinity column consisting of either anti-myc oranti-histidine monoclonal antibodies conjugated through a hydrazide orother linkage to an agarose resin and eluting with an excess of mycpeptide or histidine, respectively.

The purified recombinant protein can then be covalently cross-linked toa solid phase, such as N-hydroxysuccinimide-activated sepharose columns(Pharmacia Biotech, Piscataway, N.J.), as directed by supplier'sinstructions. These columns containing covalently linked BS249recombinant protein, can then be used to purify anti-BS249 antibodiesfrom rabbit or mouse sera (see Examples 13 and 14).

E. Coating Microtiter Plates with BS249 Expressed Proteins. Supernatantfrom a 100 mm plate, as described supra, is diluted in an appropriatevolume of PBS. Then, 100 μl of the resulting mixture is placed into eachwell of a Reacti-Bindm metal chelate microtiter plate (Pierce, Rockford,Ill.), incubated at room temperature while shaking, and followed bythree washes with 200 μl each of PBS with 0.05% Tween® 20. The preparedmicrotiter plate can then be used to screen polyclonal antisera for thepresence of BS249 antibodies (see Example 17).

Although pcDNA3.1/Myc-His is utilized in this example, it is known tothose skilled in the art that other comparable expression systems can beutilized herein with appropriate modifications in reagent and/ortechniques and are within the skill of one of ordinary skill in the art.The largest cloned insert containing the coding region of the BS249 geneis sub-cloned into either (i) a eukaryotic expression vector which maycontain, for example, a cytomegalovirus (CMV) promoter and/or proteinfusible sequences which aid in protein expression and detection, or (ii)a bacterial expression vector containing a superoxide-dismutase (SOD)and CMP-KDO synthetase (CKS) or other protein fusion gene for expressionof the protein sequence. Methods and vectors which are useful for theproduction of polypeptides which contain fusion sequences of SOD aredescribed in published EPO application No. EP 0 196 056, published Oct.1, 1986, which is incorporated herein by reference, and vectorscontaining fusion sequences of CKS are described in published EPOapplication No. EP 0 331 961, published Sep. 13, 1989, which publicationis also incorporated herein by reference. The purified protein can beused in a variety of techniques, including, but not limited to animalimmunization studies, solid phase immunoassays, etc.

Example 12 Chemical Analysis of Breast Tissue Proteins

A. Analysis of Tryptic Peptide Fragments Using MS. Sera from patientswith breast disease, such as breast cancer, sera from patients with nobreast disease, extracts of breast tissues or cells from patients withbreast disease, such as breast cancer, extracts of breast tissues orcells from patients with no breast disease, and extracts of tissues orcells from other non-diseased or diseased organs of patients are run ona polyacrylamide gel using standard procedures and stained withCoomassie Blue. Sections of the gel suspected of containing the unknownpolypeptide are excised and subjected to an in-gel reduction,acetamidation and tryptic digestion. P. Jeno et al., Anal. Bio.224:451-455 (1995) and J. Rosenfeld et al., Anal. Bio. 203:173-179(1992). The gel sections are washed with 100 mM NH₄HCO₃ andacetonitrile. The shrunken gel pieces are swollen in digestion buffer(50 mM NH₄HCO₃, 5 mM CaCl₂ and 12.5 μg/ml trypsin) at 4° C. for 45 min.The supernatant is aspirated and replaced with 5 to 10 μl of digestionbuffer without trypsin and allowed to incubate overnight at 37° C.Peptides are extracted with 3 changes of 5% formic acid and acetonitrileand evaporated to dryness. The peptides are adsorbed to approximately0.1 μl of POROS R2 sorbent (Perseptive Biosystems, Framingham,Massachusetts) trapped in the tip of a drawn gas chromatographycapillary tube by dissolving them in 10 μl of 5% formic acid and passingit through the capillary. The adsorbed peptides are washed with waterand eluted with 5% formic acid in 60% methanol. The eluant is passeddirectly into the spraying capillary of an API III mass spectrometer(Perkin-Elmer Sciex, Thornhill, Ontario, Canada) for analysis bynano-electrospray mass spectrometry. M. Wilm et al., Int. J. MassSpectrom. Ion Process 136:167-180 (1994) and M. Wilm et al., Anal. Chem.66:1-8 (1994). The masses of the tryptic peptides are determined fromthe mass spectrum obtained off the first quadruple. Masses correspondingto predicted peptides can be further analyzed in MS/MS mode to give theamino acid sequence of the peptide.

B. Peptide Fragment Analysis Using LC/MS. The presence of polypeptidespredicted from mRNA sequences found in hyperplastic disease tissues alsocan be confirmed using liquid chromatography/tandem mass spectrometry(LC/MS/MS). D. Hess et al., METHODS. A Companion to Methods inEnzymology 6:227-238 (1994). The serum specimen or tumor extract fromthe patient is denatured with SDS and reduced with dithiothreitol (1.5mg/mil) for 30 min at 90° C. followed by alkylation with iodoacetamide(4 mg/ml) for 15 min at 25° C. Following acrylamide electrophoresis, thepolypeptides are electroblotted to a cationic membrane and stained withCoomassie Blue. Following staining, the membranes are washed andsections thought to contain the unknown polypeptides are cut out anddissected into small pieces. The membranes are placed in 500 μlmicrocentrifuge tubes and immersed in 10 to 20 μl of proteolyticdigestion buffer (100 mM Tris-HCl, pH 8.2, containing 0.1 M NaCl, 10%acetonitrile, 2 mM CaCl₂ and 5 μg/ml trypsin) (Sigma, St. Louis, Mo.).After 15 hr at 37° C., 3 μl of saturated urea and 1 μt of 100 μg/mltrypsin are added and incubated for an additional 5 hr at 37° C. Thedigestion mixture is acidified with 3 μl of 10% trifluoroacetic acid andcentrifuged to separate supernatant from membrane. The supernatant isinjected directly onto a microbore, reverse phase HPLC column and elutedwith a linear gradient of acetonitrile in 0.05% trifluoroacetic acid.The eluate is fed directly into an electrospray mass spectrometer, afterpassing though a stream splitter if necessary to adjust the volume ofmaterial. The data is analyzed following the procedures set forth inExample 12, Section A.

Example 13 Gene Immunization Protocol

A. In Vivo Antigen Expression. Gene immunization circumvents proteinpurification steps by directly expressing an antigen in vivo afterinoculation of the appropriate expression vector. Also, production ofantigen by this method may allow correct protein folding andglycosylation since the protein is produced in mammalian tissue. Themethod utilizes insertion of the gene sequence into a plasmid whichcontains a CMV promoter, expansion and purification of the plasmid andinjection of the plasmid DNA into the muscle tissue of an animal.Preferred animals include mice and rabbits. See, for example, H. Daviset al., Human Molecular Genetics 2:1847-1851 (1993). After one or twobooster immunizations, the animal can then be bled, ascites fluidcollected, or the animal's spleen can be harvested for production ofhybridomas.

B. Plasmid Preparation and Purification. BS249 cDNA sequences aregenerated from the BS249 cDNA-containing vector using appropriate PCRprimers containing suitable 5′ restriction sites following theprocedures described in Example 11. The PCR product is cut withappropriate restriction enzymes and inserted into a vector whichcontains the CMV promoter (for example, pRc/CMV or pcDNA3 vectors fromInvitrogen, San Diego, Calif.). This plasmid then is expanded in theappropriate bacterial strain and purified from the cell lysate using aCsCl gradient or a Qiagen plasmid DNA purification column. All thesetechniques are familiar to one of ordinary skill in the art of molecularbiology.

C. Immunization Protocol. Anesthetized animals are immunizedintramuscularly with 0.1-100 μg of the purified plasmid diluted in PBSor other DNA uptake enhancers (Cardiotoxin, 25% sucrose). See, forexample, H. Davis et al., Human Gene Therapy 4:733-740 (1993); and P. W.Wolff et al., Biotechniques 11:474-485 (1991). One to two boosterinjections are given at monthly intervals.

D. Testing and Use of Antiserum. Animals are bled and the resultant seratested for antibody using peptides synthesized from the known genesequence (see Example 16) using techniques known in the art, such asWestern blotting or EIA techniques. Antisera produced by this method canthen be used to detect the presence of the antigen in a patient's tissueor cell extract or in a patient's serum by ELISA or Western blottingtechniques, such as those described in Examples 15 through 18.

Example 14 Production of Antibodies Against BS249

A. Production of Polyclonal Antisera. Antiserum against BS249 isprepared by injecting appropriate animals with peptides whose sequencesare derived from that of the predicted amino acid sequence of the BS249nucleotide consensus sequence (SEQUENCE ID NO 11). The synthesis ofpeptides, SEQUENCE ID NO 24, SEQUENCE ID NO 25, SEQUENCE ID NO 26, andSEQUENCE ID NO 27, was described in Example 10. Peptides used asimmunogen either can be conjugated to a carrier such as keyhole limpethemocyanine (KLH), prepared as described hereinbelow, or unconjugated(i.e., not conjugated to a carrier such as KLH).

1. Peptide Conjugation. Peptide is conjugated to maleimide activatedkeyhole limpet hemocyanine (KLH, commercially available as Imject®,available from Pierce Chemical Company, Rockford, Ill.). Imject®contains about 250 moles of reactive maleimide groups per mole ofhemocyanine. The activated KLH is dissolved in phosphate buffered saline(PBS, pH 8.4) at a concentration of about 7.7 mg/ml. The peptide isconjugated through cysteines occurring in the peptide sequence, or to acysteine previously added to the synthesized peptide in order to providea point of attachment. The peptide is dissolved in dimethyl sulfoxide(DMSO, Sigma Chemical Company, St. Louis, Mo.) and reacted with theactivated KLH at a mole ratio of about 1.5 moles of peptide per mole ofreactive maleimide attached to the KLH. A procedure for the conjugationof peptide (SEQUENCE ID NO 24) is provided hereinbelow. It is known tothe ordinary artisan that the amounts, times and conditions of such aprocedure can be varied to optimize peptide conjugation.

The conjugation reaction described hereinbelow is based on obtaining 3mg of KLH peptide conjugate (“conjugated peptide”), which contains about0.77 μmoles of reactive maleimide groups. This quantity of peptideconjugate usually is adequate for one primary injection and four boosterinjections for production of polyclonal antisera in a rabbit. Briefly,peptide (SEQUENCE ID NO 24) is dissolved in DMSO at a concentration of1.16 μmoles/100 μl of DMSO. One hundred microliters (100 μl) of the DMSOsolution are added to 380 μl of the activated KLH solution prepared asdescribed hereinabove, and 20 μl of PBS (pH 8.4) are added to bring thevolume to 500 μl. The reaction is incubated overnight at roomtemperature with stirring. The extent of reaction is determined bymeasuring the amount of unreacted thiol in the reaction mixture. Thedifference between the starting concentration of thiol and the finalconcentration is assumed to be the concentration of peptide which hascoupled to the activated KLH. The amount of remaining thiol is measuredusing Ellman's reagent (5,5′-dithiobis(2-nitrobenzoic acid), PierceChemical Company, Rockford, Ill.). Cysteine standards are made at aconcentration of 0, 0.1, 0.5, 2, 5 and 20 mM by dissolving 35 mg ofcysteine HCl (Pierce Chemical Company, Rockford, Ill.) in 10 ml of PBS(pH 7.2) and diluting the stock solution to the desiredconcentration(s). The photometric determination of the concentration ofthiol is accomplished by placing 200 μl of PBS (pH 8.4) in each well ofan Immulon 2® microwell plate (Dynex Technologies, Chantilly, Va.).Next, 10 μl of standard or reaction mixture is added to each well.Finally, 20 μl of Ellman's reagent at a concentration of 1 mg/ml in PBS(pH 8.4) is added to each well. The wells are incubated for 10 minutesat room temperature, and the absorbance of all wells is read at 415 nmwith a microplate reader (such as the BioRad Model 3550, BioRad,Richmond, Calif.). The absorbance of the standards is used to constructa standard curve and the thiol concentration of the reaction mixture isdetermined from the standard curve. A decrease in the concentration offree thiol is indicative of a successful conjugation reaction. Unreactedpeptide is removed by dialysis against PBS (pH 7.2) at room temperaturefor 6 hours. The conjugate is stored at 2-8° C. if it is to be usedimmediately; otherwise, it is stored at −20° C. or colder.

2. Animal Immunization. Female white New Zealand rabbits weighing 2 kgor more are used for raising polyclonal antiserum. Generally, one animalis immunized per unconjugated or conjugated peptide (prepared asdescribed hereinabove). One week prior to the first immunization, 5 to10 ml of blood is obtained from the animal to serve as a non-immuneprebleed sample.

Unconjugated or conjugated peptide is used to prepare the primaryimmunogen by emulsifying 0.5 ml of the peptide at a concentration of 2mg/ml in PBS (pH 7.2) which contains 0.5 ml of complete Freund'sadjuvant (CFA) (Difco, Detroit, Mich.). The immunogen is injected intoseveral sites of the animal via subcutaneous, intraperitoneal, and/orintramuscular routes of administration. Four weeks following the primaryimmunization, a booster immunization is administered. The immunogen usedfor the booster immunization dose is prepared by emulsifying 0.5 ml ofthe same unconjugated or conjugated peptide used for the primaryimmunogen, except that the peptide now is diluted to 1 mg/ml with 0.5 mlof incomplete Freund's adjuvant (IFA) (Difco, Detroit, Mich.). Again,the booster dose is administered into several sites and can utilizesubcutaneous, intraperitoneal and intramuscular types of injections. Theanimal is bled (5 ml) two weeks after the booster immunization and theserum is tested for immunoreactivity to the peptide, as described below.The booster and bleed schedule is repeated at 4 week intervals until anadequate titer is obtained. The titer or concentration of antiserum isdetermined by microtiter EIA as described in Example 17, below. Anantibody titer of 1:500 or greater is considered an adequate titer forfurther use and study.

B. Production of Monoclonal Antibody

1. Immunization Protocol. Mice are immunized using immunogens preparedas described hereinabove, except that the amount of the unconjugated orconjugated peptide for monoclonal antibody production in mice isone-tenth the amount used to produce polyclonal antisera in rabbits.Thus, the primary immunogen consists of 100 μg of unconjugated orconjugated peptide in 0.1 ml of CFA emulsion; while the immunogen usedfor booster immunizations consists of 50 μg of unconjugated orconjugated peptide in 0.1 ml of IFA. Hybridomas for the generation ofmonoclonal antibodies are prepared and screened using standardtechniques. The methods used for monoclonal antibody development followprocedures known in the art such as those detailed in Kohler andMilstein, Nature 256:494 (1975) and reviewed in J. G. R. Hurrel, ed.,Monoclonal Hybridoma Antibodies: Techniques and Applications, CRC Press,Inc., Boca Raton, Fla. (1982). Another method of monoclonal antibodydevelopment which is based on the Kohler and Milstein method is that ofL. T. Mimms et al., Virology 176:604-619 (1990), which is incorporatedherein by reference.

The immunization regimen (per mouse) consists of a primary immunizationwith additional booster immunizations. The primary immunogen used forthe primary immunization consists of 100 μg of unconjugated orconjugated peptide in 50 μl of PBS (pH 7.2) previously emulsified in 50μl of CFA. Booster immunizations performed at approximately two weeksand four weeks post primary immunization consist of 50 μg ofunconjugated or conjugated peptide in 50 μl of PBS (pH 7.2) emulsifiedwith 50 μl IFA. A total of 100 μl of this immunogen is inoculatedintraperitoneally and subcutaneously into each mouse. Individual miceare screened for immune response by microtiter plate enzyme immunoassay(EIA) as described in Example 17 approximately four weeks after thethird immunization. Mice are inoculated either intravenously,intrasplenically or intraperitoneally with 50 μg of unconjugated orconjugated peptide in PBS (pH 7.2) approximately fifteen weeks after thethird immunization.

Three days after this intravenous boost, splenocytes are fused with, forexample, Sp2/0-Ag14 myeloma cells (Milstein Laboratories, England) usingthe polyethylene glycol (PEG) method. The fusions are cultured inIscove's Modified Dulbecco's Medium (IMDM) containing 10% fetal calfserum (FCS), plus 1% hypoxanthine, aminopterin and thymidine (HAT). Bulkcultures are screened by microtiter plate EIA following the protocol inExample 17. Clones reactive with the peptide used an immunogen andnon-reactive with other peptides (i.e., peptides of BS249 not used asthe immunogen) are selected for final expansion. Clones thus selectedare expanded, aliquoted and frozen in IMDM containing 10% FCS and 10%dimethyl-sulfoxide.

2. Production of Ascites Fluid Containing Monoclonal Antibodies. Frozenhybridoma cells prepared as described hereinabove are thawed and placedinto expansion culture. Viable hybridoma cells are inoculatedintraperitoneally into Pristane treated mice. Ascitic fluid is removedfrom the mice, pooled, filtered through a 0.2μ filter and subjected toan immunoglobulin class G (IgG) analysis to determine the volume of theProtein A column required for the purification.

3. Purification of Monoclonal Antibodies From Ascites Fluid. Briefly,filtered and thawed ascites fluid is mixed with an equal volume ofProtein A sepharose binding buffer (1.5 M glycine, 3.0 M NaCl, pH 8.9)and refiltered through a 0.2μ filter. The volume of the Protein A columnis determined by the quantity of IgG present in the ascites fluid. Theeluate then is dialyzed against PBS (pH 7.2) overnight at 2-8° C. Thedialyzed monoclonal antibody is sterile filtered and dispensed inaliquots. The immunoreactivity of the purified monoclonal antibody isconfirmed by determining its ability to specifically bind to the peptideused as the immunogen by use of the EIA microtiter plate assay procedureof Example 17. The specificity of the purified monoclonal antibody isconfirmed by determining its lack of binding to irrelevant peptides suchas peptides of BS249 not used as the immunogen. The purified anti-BS249monoclonal thus prepared and characterized is placed at either 2-8° C.for short term storage or at −80° C. for long term storage.

4. Further Characterization of Monoclonal Antibody. The isotype andsubtype of the monoclonal antibody produced as described hereinabove canbe determined using commercially available kits (available fromAmersham. Inc., Arlington Heights, Ill.). Stability testing also can beperformed on the monoclonal antibody by placing an aliquot of themonoclonal antibody in continuous storage at 2-8° C. and assayingoptical density (OD) readings throughout the course of a given period oftime.

C. Use of Recombinant Proteins as Immunogens. It is within the scope ofthe present invention that recombinant proteins made as described hereincan be utilized as immunogens in the production of polyclonal andmonoclonal antibodies, with corresponding changes in reagents andtechniques known to those skilled in the art.

Example 15 Purification of Serum Antibodies Which Specifically Bind toBS249 Peptides

Immune sera, obtained as described hereinabove in Examples 13 and/or 14,is affinity purified using immobilized synthetic peptides prepared asdescribed in Example 10, or recombinant proteins prepared as describedin Example 11. An IgG fraction of the antiserum is obtained by passingthe diluted, crude antiserum over a Protein A column (Affi-Gel proteinA, Bio-Rad, Hercules, Calif.). Elution with a buffer (Binding Buffer,supplied by the manufacturer) removes substantially all proteins thatare not immunoglobulins. Elution with 0.1 M buffered glycine (pH 3)gives an immunoglobulin preparation that is substantially free ofalbumin and other serum proteins.

Immunoaffinity chromatography is performed to obtain a preparation witha higher fraction of specific antigen-binding antibody. The peptide usedto raise the antiserum is immobilized on a chromatography resin, and thespecific antibodies directed against its epitopes are adsorbed to theresin. After washing away non-binding components, the specificantibodies are eluted with 0.1 M glycine buffer, pH 2.3. Antibodyfractions are immediately neutralized with 1.0M Tris buffer (pH 8.0) topreserve immunoreactivity. The chromatography resin chosen depends onthe reactive groups present in the peptide. If the peptide has an aminogroup, a resin such as Affi-Gel 10 or Affi-Gel 15 is used (Bio-Rad,Hercules, Calif.). If coupling through a carboxy group on the peptide isdesired, Affi-Gel 102 can be used (Bio-Rad, Hercules, Calif.). If thepeptide has a free sulfhydryl group, an organomercurial resin such asAffi-Gel 501 can be used (Bio-Rad, Hercules, Calif.).

Alternatively, spleens can be harvested and used in the production ofhybridomas to produce monoclonal antibodies following routine methodsknown in the art as described hereinabove.

Example 16 Western Blotting of Tissue Samples

Protein extracts are prepared by homogenizing tissue samples in 0.1 MTris-HCl (pH 7.5), 15% (w/v) glycerol, 0.2 mM EDTA, 1.0 mM1,4-dithiothreitol, 10 μg/ml leupeptin and 1.0 mMphenylmethylsulfonylfluoride [Kain et al., Biotechniques, 17:982(1994)]. Following homogenization, the homogenates are centrifuged at 4°C. for 5 minutes to separate supernatant from debris. Debris isreextracted by homogenization with a buffer that is similar to abovealso contains 0.1 M Tricine and 0.1% SDS. The supernatant from thesecond extraction is used for Western blotting. For proteinquantitation, 2-5 μl of supernatant are added to 1.5 ml of CoomassieProtein Reagent (Pierce, Rockford, Ill.), and the resulting absorbanceat 595 nm is measured.

For SDS-PAGE, samples are adjusted to desired protein concentration withTricine Buffer (Novex, San Diego, Calif.), mixed with an equal volume of2× Tricine sample buffer (Novex, San Diego, Calif.), and heated for 5minutes at 100° C. in a thermal cycler. Samples are then applied to aNovex 10-20% Precast Tricine Gel for electrophoresis. Followingelectrophoresis, samples are transferred from the gels to nitrocellulosemembranes in Novex Tris-Glycine Transfer buffer. Membranes are thenprobed with specific anti-peptide antibodies using the reagents andprocedures provided in the Western Lights or Western Lights Plus(Tropix, Bedford, Mass.) chemiluminesence detection kits.Chemiluminesent bands are visualized by exposing the developed membranesto Hyperfilm ECL (Amersham, Arlington Heights, Ill.).

Competition experiments are carried out in an analogous manner as above,with the following exception; the primary antibodies (anti-peptidepolyclonal antisera) are pre-incubated for 30 minutes at roomtemperature with varying concentrations of peptide immunogen prior toexposure to the nitrocellulose filter. Development of the Western isperformed as above.

After visualization of the bands on film, the bands can also bevisualized directly on the membranes by the addition and development ofa chromogenic substrate such as 5-bromo-4-chloro-3-indolyl phosphate(BCIP). This chromogenic solution contains 0.016% BCIP in a solutioncontaining 100 mM NaCl, 5 mM MgCl₂ and 100 mM Tris-HCl (pH 9.5). Thefilter is incubated in the solution at room temperature until the bandsdevelop to the desired intensity. Molecular mass determination is madebased upon the mobility of pre-stained molecular weight standards(Novex, San Diego, Calif.) or biotinylated molecular weight standards(Tropix, Bedford, Mass.).

Example 17 EIA Microtiter Plate Assay

The immunoreactivity of antiserum preferably obtained from rabbits ormice as described in Example 13 or Example 14 is determined by means ofa microtiter plate EIA, as follows. Briefly, synthetic peptides,SEQUENCE ID NO 24, SEQUENCE ID NO 25, SEQUENCE ID NO 26 and SEQUENCE IDNO 27, prepared as described in Example 10, are dissolved in 50 mMcarbonate buffer (pH 9.6) to a final concentration of 2 μg/ml. Next, 100μl of the peptide or protein solution are placed in each well of anImmulon 2® microtiter plate (Dynex Technologies, Chantilly, Va.). Theplate is incubated overnight at room temperature and then washed fourtimes with deionized water. The wells are blocked by adding 125 μl of asuitable protein blocking agent, such as Superblock® (Pierce ChemicalCompany, Rockford, Ill.), in phosphate buffered saline (PBS, pH 7.4) toeach well and then immediately discarding the solution. This blockingprocedure is performed three times. Antiserum obtained from immunizedrabbits or mice prepared as previously described is diluted in a proteinblocking agent (e.g., a 3% Superblock® solution) in PBS containing 0.05%Tween-20® (monolaurate polyoxyethylene ether) (Sigma Chemical Company,St. Louis, Mo.) and 0.05% sodium azide at dilutions of 1:100, 1:500,1:2500, 1:12,500, and 1:62,500 and placed in each well of the coatedmicrotiter plate. The wells then are incubated for three hours at roomtemperature. Each well is washed four times with deionized water. Onehundred μl of alkaline phosphatase-conjugated goat anti-rabbit IgG orgoat anti-mouse IgG antiserum (Southern Biotech, Birmingham, Ala.),diluted 1:2000 in 3% Superblock® solution in phosphate buffered salinecontaining 0.05% Tween 20® and 0.05% sodium azide, is added to eachwell. The wells are incubated for two hours at room temperature. Next,each well is washed four times with deionized water. One hundredmicroliters (100 μl) of paranitrophenyl phosphate substrate (Kirkegaardand Perry Laboratories, Gaithersburg, Md.) then are added to each well.The wells are incubated for thirty minutes at room temperature. Theabsorbance at 405 nm is read of each well. Positive reactions areidentified by an increase in absorbance at 405 nm in the test well abovethat absorbance given by a non-immune serum (negative control). Apositive reaction is indicative of the presence of detectable anti-BS249antibodies. Titers of the anti-peptide antisera are calculated from thepreviously described dilutions of antisera and defined as the calculateddilution, where A_(405nm)=0.5 OD.

In addition to titers, apparent affinities [K_(d)(app)] may also bedetermined for some of the anti-peptide antisera. EIA microtiter plateassay results can be used to derive the apparent dissociation constants(K_(d)) based on an analog of the Michaelis-Menten equation [V. VanHeyningen, Methods in Enzymology, Vol. 121, p. 472 (1986) and furtherdescribed in X. Qiu, et al., Journal of Immunology, Vol. 156, p. 3350(1996)]:$\left\lbrack {{Ag} - {Ab}} \right\rbrack = {\left\lbrack {{Ag} - {Ab}} \right\rbrack_{\max} \times \frac{\lbrack{Ab}\rbrack}{\lbrack{Ab}\rbrack = K_{d}}}$

Where [Ag-Ab] is the antigen-antibody complex concentration,[Ag-Ab]_(max) is the maximum complex concentration, [Ab] is the antibodyconcentration, and K_(d) is the dissociation constant. During the curvefitting, the [Ag-Ab] is replaced with the background subtracted value ofthe OD_(405nm) at the given concentration of Ab. Both K_(d) and[OD_(405 nm)]_(max), which corresponds to the [Ag-Ab]_(max), are treatedas fitted parameters. The software program Origin can be used for thecurve fitting.

Example 18 Coating of Solid Phase Particles

A. Coating of Microparticles with Antibodies Which Specifically Bind toBS249 Antigen. Affinity purified antibodies which specifically bind toBS249 protein (see Example 15) are coated onto microparticles ofpolystyrene, carboxylated polystyrene, polymethylacrylate or similarparticles having a radius in the range of about 0.1 to 20 μm.Microparticles may be either passively or actively coated. One coatingmethod comprises coating EDAC(1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (AldrichChemical Co., Milwaukee, Wis.) activated carboxylated latexmicroparticles with antibodies which specifically bind to BS249 protein,as follows. Briefly, a final 0.375% solid suspension of resin washedcarboxylated latex microparticles (available from Bangs Laboratories,Carmel, IN or Serodyn, Indianapolis, Ind.) are mixed in a solutioncontaining 50 mM MES buffer, pH 4.0 and 150 mg/l of affinity purifiedanti-BS249 antibody (see Example 14) for 15 min in an appropriatecontainer. EDAC coupling agent is added to a final concentration of 5.5μg/ml to the mixture and mixed for 2.5 hr at room temperature.

The microparticles then are washed with 8 volumes of a Tween 20®/sodiumphosphate wash buffer (pH 7.2) by tangential flow filtration using a 0.2μm Microgon Filtration module. Washed microparticles are stored in anappropriate buffer which usually contains a dilute surfactant andirrelevant protein as a blocking agent, until needed.

B. Coating of ¼ Inch Beads. Antibodies which specifically bind toBS249-antigen also may be coated on the surface of ¼ inch polystyrenebeads by routine methods known in the art (Snitman et al., U.S. Pat. No.5,273,882, incorporated herein by reference) and used in competitivebinding or EIA sandwich assays.

Polystyrene beads first are cleaned by ultrasonicating them for about 15seconds in 10 mM NaHCO₃ buffer at pH 8.0. The beads then are washed indeionized water until all fines are removed. Beads then are immersed inan antibody solution in 10 mM carbonate buffer, pH 8 to 9.5. Theantibody solution can be as dilute as 1 μg/ml in the case of highaffinity monoclonal antibodies or as concentrated as about 500 μg/ml forpolyclonal antibodies which have not been affinity purified. Beads arecoated for at least 12 hours at room temperature, and then they arewashed with deionized water. Beads may be air dried or stored wet (inPBS, pH 7.4). They also may be overcoated with protein stabilizers (suchas sucrose) or protein blocking agents used as non-specific bindingblockers (such as irrelevant proteins, Carnation skim milk, Superblock®,or the like).

Example 19 Microparticle Enzyme Immunoassay (MEIA)

BS249 antigens are detected in patient test samples by performing astandard antigen competition EIA or antibody sandwich EIA and utilizinga solid phase such as microparticles (MEIA). The assay can be performedon an automated analyzer such as the IMx® Analyzer (Abbott Laboratories,Abbott Park, Ill.).

A. Antibody Sandwich EIA. Briefly, samples suspected of containing BS249antigen are incubated in the presence of anti-BS249 antibody-coatedmicroparticles (prepared as described in Example 17) in order to formantigen/antibody complexes. The microparticles then are washed and anindicator reagent comprising an antibody conjugated to a signalgenerating compound (i.e., enzymes such as alkaline phosphatase orhorseradish peroxide) is added to the antigen/antibody complexes or themicroparticles and incubated. The microparticles are washed and thebound antibody/antigen/antibody complexes are detected by adding asubstrate (e.g., 4-methyl umbelliferyl phosphate (MUP), or OPD/peroxide,respectively), that reacts with the signal generating compound togenerate a measurable signal. An elevated signal in the test sample,compared to the signal generated by a negative control, detects thepresence of BS249 antigen. The presence of BS249 antigen in the testsample is indicative of a diagnosis of a breast disease or condition,such as breast cancer.

B. Competitive Binding Assay. The competitive binding assay uses apeptide or protein that generates a measurable signal when the labeledpeptide is contacted with an anti-peptide antibody coated microparticle.This assay can be performed on the IMx® Analyzer (available from AbbottLaboratories, Abbott Park, Ill.). The labeled peptide is added to theBS249 antibody-coated microparticles (prepared as described in Example17) in the presence of a test sample suspected of containing BS249antigen, and incubated for a time and under conditions sufficient toform labeled BS249 peptide (or labeled protein)/bound antibody complexesand/or patient BS249 antigen/bound antibody complexes. The BS249 antigenin the test sample competes with the labeled BS249 peptide (or BS249protein) for binding sites on the microparticle. BS249 antigen in thetest sample results in a lowered binding of labeled peptide and antibodycoated microparticles in the assay since antigen in the test sample andthe BS249 peptide or BS249 protein compete for antibody binding sites. Alowered signal (compared to a control) indicates the presence of BS249antigen in the test sample. The presence of BS249 antigen suggests thediagnosis of a breast disease or condition, such as breast cancer.

The BS249 polynucleotides and the proteins encoded thereby which areprovided and discussed hereinabove are useful as markers of breasttissue disease, especially breast cancer. Tests based upon theappearance of this marker in a test sample such as blood, plasma orserum can provide low cost, non-invasive, diagnostic information to aidthe physician to make a diagnosis of cancer, to help select a therapyprotocol, or to monitor the success of a chosen therapy. This marker mayappear in readily accessible body fluids such as blood, urine or stoolas antigens derived from the diseased tissue which are detectable byimmunological methods. This marker may be elevated in a disease state,altered in a disease state, or be a normal protein of the breast whichappears in an inappropriate body compartment.

Example 20 Immunohistochemical Detection of BS249 Protein

Antiserum against a BS249 synthetic peptide derived from the consensuspeptide sequence (SEQUENCE ID NO 23) described in Example 14, above, isused to immunohistochemically stain a variety of normal and diseasedtissues using standard procedures. Briefly, frozen blocks of tissue arecut into 6 micron sections, and placed on microscope slides. Afterfixation in cold acetone, the sections are dried at room temperature,then washed with phosphate buffered saline and blocked. The slides areincubated with the antiserum against a synthetic peptide derived fromthe consensus BS249 peptide sequence (SEQUENCE ID NO 23) at a dilutionof 1:500, washed, incubated with biotinylated goat anti-rabbit antibody,washed again, and incubated with avidin labeled with horseradishperoxidase. After a final wash, the slides are incubated with3-amino-9-ethylcarbazole substrate which gives a red stain. The slidesare counterstained with hematoxylin, mounted, and examined under amicroscope by a pathologist.

                   #             SEQUENCE LISTING<160> NUMBER OF SEQ ID NOS: 29 <210> SEQ ID NO 1 <211> LENGTH: 285<212> TYPE: DNA <213> ORGANISM: Homo sapiens <220> FEATURE:<221> NAME/KEY: base_polymorphism <222> LOCATION: 6<223> OTHER INFORMATION: /note = “′n′  #represents an a or g or t or c      polymorphism at this position <400> SEQUENCE: 1gaggangagg aggaagaggg gagcacaaag gatccaggtc tcccgacggg ag#gttaatac     60caagaaccat gtgtgccgag cggctgggcc agttcatgac cctggctttg gt#gttggcca    120cctttgaccc ggcgcggggg accgacgcca ccaacccacc cgagggtccc ca#agacagga    180gctcccagca gaaaggccgc ctgtccctgc agaatacagc ggagatccag ca#ctgtttgg    240 tcaacgctgg cgatgtgggg tgtggcgtgt ttgaatgttt cgaga   #                 285 <210> SEQ ID NO 2 <211> LENGTH: 257<212> TYPE: DNA <213> ORGANISM: Homo sapiens <400> SEQUENCE: 2gtttgaatgt ttcgagaaca actcttgtga gattcggggc ttacatggga tt#tgcatgac     60ttttctgcac aacgctggaa aatttgatgc ccagggcaag tcattcatca aa#gacgcctt    120gaaatgtaag gcccacgctc tgcggcacag gttcggctgc ataagccgga ag#tgcccggc    180catcagggaa atggtgtccc agttgcagcg ggaatgctac ctcaagcacg ac#ctgtgcgc    240 ggctgcccag gagaaca              #                  #                   #  257 <210> SEQ ID NO 3 <211> LENGTH: 246<212> TYPE: DNA <213> ORGANISM: Homo sapiens <400> SEQUENCE: 3ctggaaaatt tgatgcccag ggcaagtcat tcatcaaaga cgccttgaaa tg#taaggccc     60acgctctgcg gcacaggttc ggctgcataa gccggaagtg cccggccatc ag#ggaaatgg    120tgtcccagtt gcagcgggaa tgctacctca agcacgacct gtgcgcggct gc#ccaggaga    180acacccgggt gatagtggag atgatccatt tcaaggactt gctgctgcac ga#accctacg    240 tggacc                  #                  #                   #          246 <210> SEQ ID NO 4 <211> LENGTH: 292<212> TYPE: DNA <213> ORGANISM: Homo sapiens <400> SEQUENCE: 4atccatttca aggacttgct gctgcacgaa ccctacgtgg acctcgtgaa ct#tgctgctg     60acctgtgggg aggaggtgaa ggaggccatc acccacagcg tgcaggttca gt#gtgagcag    120aactggggaa gcctgtgctc catcttgagc ttctgcacct cggccatcca ga#agcctccc    180acggcgcccc ccgagcgcca gccccaggtg gacagaacca agctctccag gg#cccaccac    240ggggaagcag gacatcacct cccagagccc agcagtaggg agatggccga gg#            292 <210> SEQ ID NO 5 <211> LENGTH: 301 <212> TYPE: DNA<213> ORGANISM: Homo sapiens <400> SEQUENCE: 5agaaccaagc tctccagggc ccaccacggg gaagcaggac atcacctccc ag#agcccagc     60agtagggaga ctggccgagg tgccaagggt gagcgaggta gcaagagcca cc#caaacgcc    120catgcccgag gcagagtcgg gggccttggg gctcagggac cttccggaag ca#gcgagtgg    180gaagacgaac agtctgagta ttctgatatc cggaggtgaa atgaaaggcc tg#gccacgaa    240atctttcctc cacgccgtcc attttcttat ctatggacat tccaaaacat tt#accattag    300 a                   #                  #                   #              301 <210> SEQ ID NO 6<211> LENGTH: 229 <212> TYPE: DNA <213> ORGANISM: Homo sapiens<220> FEATURE: <221> NAME/KEY: base_polymorphism <222> LOCATION: 99<223> OTHER INFORMATION: /note = ”′n′  #represents an a or g or t or c      polymorphism at this position <220> FEATURE:<221> NAME/KEY: base_polymorphism <222> LOCATION: 100<223> OTHER INFORMATION: /note = “′n′  #represents an a or g or t or c      polymorphism at this position <400> SEQUENCE: 6ctgatatccg gaggtgaaat gaaaggcctg gccacgaaat ctttcctcca cg#ccgtccat     60tttcttatct atggacattc caaaacattt accattagnn aggggggatg tc#acacgcag    120gattctgtgg ggactgtgga cttcatcgag gtgtgtgttc gcggaacgga ca#ggtgagat    180 ggagacccct ggggccgtgg ggtctcaggg gtgcctggtg aattctgca  #              229 <210> SEQ ID NO 7 <211> LENGTH: 262 <212> TYPE: DNA<213> ORGANISM: Homo sapiens <400> SEQUENCE: 7gtgagatgga gacccctggg gccgtggggt ctcaggggtg cctggtgaat tc#tgcactta     60cacgtactca agggagcgcg cccgcgttat cctcgtacct ttgtcttctt tc#catctgtg    120gagtcagtgg gtgtcggccg ctctgttgtg ggggaggtga accagggagg gg#cagggcaa    180ggcagggccc ccagagctgg gccacacagt gggtgctggg cctcgccccg aa#gcttctgg    240 tgcagcagcc tctggtgctt ca            #                  #                262 <210> SEQ ID NO 8 <211> LENGTH: 242 <212> TYPE: DNA<213> ORGANISM: Homo sapiens <220> FEATURE:<221> NAME/KEY: base_polymorphism <222> LOCATION: 46<223> OTHER INFORMATION: /note = ”′n′  #represents an a or g or t or c      polymorphism at this position <220> FEATURE:<221> NAME/KEY: base_polymorphism <222> LOCATION: 92<223> OTHER INFORMATION: /note = “′n′  #represents an a or g or t or c      polymorphism at this position <220> FEATURE:<221> NAME/KEY: base_polymorphism <222> LOCATION: 94<223> OTHER INFORMATION: /note = ”′n′  #represents an a or g or t or c      polymorphism at this position <220> FEATURE:<221> NAME/KEY: base_polymorphism <222> LOCATION: 188<223> OTHER INFORMATION: /note = “′n′  #represents an a or g or t or c      polymorphism at this position <220> FEATURE:<221> NAME/KEY: base_polymorphism <222> LOCATION: 190<223> OTHER INFORMATION: /note = ”′n′  #represents an a or g or t or c      polymorphism at this position <400> SEQUENCE: 8gcagcctctg gtgctgtctc cgcggaagtc agggcggctg gattcnagga ca#ggagtgaa     60tgtaaaaata aatatcgctt agaatgcagg anangggtgg agaggaggca gg#ggccgagg    120gggtgcttgg tgccaaactg aaattcagtt tcttgtgtgg ggccttgcgg tt#cagagctc    180ttggcgangn tggagggagg agtgtcattt ctatgtgtaa tttctgagcc at#tgtactgt    240 ct                   #                  #                   #             242 <210> SEQ ID NO 9<211> LENGTH: 247 <212> TYPE: DNA <213> ORGANISM: Homo sapiens<400> SEQUENCE: 9gtttgaaagc catttattta gatgacagat atgtagatat aactggataa at#aaaaaaag     60tgaaatcgag atttgaagca gtggttaaaa tataaactca taggggccac tc#ccttggac    120agtgtccccc ccagcccaga cagtacaatg gctcagaaat tacacataga aa#tgacactc    180ctccctccac cctcgccaag agctctgaac cgcaaggccc cacacaagaa ac#tgaatttc    240 agtttgg                  #                  #                   #         247 <210> SEQ ID NO 10 <211> LENGTH: 1760<212> TYPE: DNA <213> ORGANISM: Homo sapiens <400> SEQUENCE: 10gaggaggagg aggaggaaga ggggagcaca aaggatccag gtctcccgac gg#gaggttaa     60taccaagaac catgtgtgcc gagcggctgg gccagttcat gaccctggct tt#ggtgttgg    120ccacctttga cccggcgcgg gggaccgacg ccaccaaccc acccgagggt cc#ccaagaca    180ggagctccca gcagaaaggc cgcctgtccc tgcagaatac agcggagatc ca#gcactgtt    240tggtcaacgc tggcgatgtg gggtgtggcg tgtttgaatg tttcgagaac aa#ctcttgtg    300agattcgggg cttacatggg atttgcatga cttttctgca caacgctgga aa#atttgatg    360cccagggcaa gtcattcatc aaagacgcct tgaaatgtaa ggcccacgct ct#gcggcaca    420ggttcggctg cataagccgg aagtgcccgg ccatcaggga aatggtgtcc ca#gttgcagc    480gggaatgcta cctcaagcac gacctgtgcg cggctgccca ggagaacacc cg#ggtgatag    540tggagatgat ccatttcaag gacttgctgc tgcacgaacc ctacgtggac ct#cgtgaact    600tgctgctgac ctgtggggag gaggtgaagg aggccatcac ccacagcgtg ca#ggttcagt    660gtgagcagaa ctggggaagc ctgtgctcca tcttgagctt ctgcacctcg gc#catccaga    720agcctcccac ggcgcccccc gagcgccagc cccaggtgga cagaaccaag ct#ctccaggg    780cccaccacgg ggaagcagga catcacctcc cagagcccag cagtagggag ac#tggccgag    840gtgccaaggg tgagcgaggt agcaagagcc acccaaacgc ccatgcccga gg#cagagtcg    900ggggccttgg ggctcaggga ccttccggaa gcagcgagtg ggaagacgaa ca#gtctgagt    960attctgatat ccggaggtga aatgaaaggc ctggccacga aatctttcct cc#acgccgtc   1020cattttctta tctatggaca ttccaaaaca tttaccatta gagagggggg at#gtcacacg   1080caggattctg tggggactgt ggacttcatc gaggtgtgtg ttcgcggaac gg#acaggtga   1140gatggagacc cctggggccg tggggtctca ggggtgcctg gtgaattctg ca#cttacacg   1200tactcaaggg agcgcgcccg cgttatcctc gtacctttgt cttctttcca tc#tgtggagt   1260cagtgggtgt cggccgctct gttgtggggg aggtgaacca gggaggggca gg#gcaaggca   1320gggcccccag agctgggcca cacagtgggt gctgggcctc gccccgaagc tt#ctggtgca   1380gcagcctctg gtgctgtctc cgcggaagtc agggcggctg gattccagga ca#ggagtgaa   1440tgtaaaaata aatatcgctt agaatgcagg agaagggtgg agaggaggca gg#ggccgagg   1500gggtgcttgg tgccaaactg aaattcagtt tcttgtgtgg ggccttgcgg tt#cagagctc   1560ttggcgaggg tggagggagg agtgtcattt ctatgtgtaa tttctgagcc at#tgtactgt   1620ctgggctggg ggggacactg tccaagggag tggcccctat gagtttatat tt#taaccact   1680gcttcaaatc tcgatttcac tttttttatt tatccagtta tatctacata tc#tgtcatct   1740 aaataaatgg ctttcaaaca             #                  #                 176 #0 <210> SEQ ID NO 11 <211> LENGTH: 1756<212> TYPE: DNA <213> ORGANISM: Homo sapiens <400> SEQUENCE: 11gaggaggagg aggaagaggg gagcacaaag gatccaggtc tcccgacggg ag#gttaatac     60caagaaccat gtgtgccgag cggctgggcc agttcatgac cctggctttg gt#gttggcca    120cctttgaccc ggcgcggggg accgacgcca ccaacccacc cgagggtccc ca#agacagga    180gctcccagca gaaaggccgc ctgtccctgc agaatacagc ggagatccag ca#ctgtttgg    240tcaacgctgg cgatgtgggg tgtggcgtgt ttgaatgttt cgagaacaac tc#ttgtgaga    300ttcggggctt acatgggatt tgcatgactt ttctgcacaa cgctggaaaa tt#tgatgccc    360agggcaagtc attcatcaaa gacgccttga aatgtaaggc ccacgctctg cg#gcacaggt    420tcggctgcat aagccggaag tgcccggcca tcagggaaat ggtgtcccag tt#gcagcggg    480aatgctacct caagcacgac ctgtgcgcgg ctgcccagga gaacacccgg gt#gatagtgg    540agatgatcca tttcaaggac ttgctgctgc acgaacccta cgtggacctc gt#gaacttgc    600tgctgacctg tggggaggag gtgaaggagg ccatcaccca cagcgtgcag gt#tcagtgtg    660agcagaactg gggaagcctg tgctccatct tgagcttctg cacctcggcc at#ccagaagc    720ctcccacggc gccccccgag cgccagcccc aggtggacag aaccaagctc tc#cagggccc    780accacgggga agcaggacat cacctcccag agcccagcag tagggagact gg#ccgaggtg    840ccaagggtga gcgaggtagc aagagccacc caaacgccca tgcccgaggc ag#agtcgggg    900gccttggggc tcagggacct tccggaagca gcgagtggga agacgaacag tc#tgagtatt    960ctgatatccg gaggtgaaat gaaaggcctg gccacgaaat ctttcctcca cg#ccgtccat   1020tttcttatct atggacattc caaaacattt accattagag aggggggatg tc#acacgcag   1080gattctgtgg ggactgtgga cttcatcgag gtgtgtgttc gcggaacgga ca#ggtgagat   1140ggagacccct ggggccgtgg ggtctcaggg gtgcctggtg aattctgcac tt#acacgtac   1200tcaagggagc gcgcccgcgt tatcctcgta cctttgtctt ctttccatct gt#ggagtcag   1260tgggtgtcgg ccgctctgtt gtgggggagg tgaaccaggg aggggcaggg ca#aggcaggg   1320cccccagagc tgggccacac agtgggtgct gggcctcgcc ccgaagcttc tg#gtgcagca   1380gcctctggtg ctgtctccgc ggaagtcagg gcggctggat tccaggacag ga#gtgaatgt   1440aaaaataaat atcgcttaga atgcaggaga agggtggaga ggaggcaggg gc#cgaggggg   1500tgcttggtgc caaactgaaa ttcagtttct tgtgtggggc cttgcggttc ag#agctcttg   1560gcgagggtgg agggaggagt gtcatttcta tgtgtaattt ctgagccatt gt#actgtctg   1620ggctgggggg gacactgtcc aagggagtgg cccctatgag tttatatttt aa#ccactgct   1680tcaaatctcg atttcacttt ttttatttat ccagttatat ctacatatct gt#catctaaa   1740 taaatggctt tcaaac              #                  #                   #  1756 <210> SEQ ID NO 12 <211> LENGTH: 68<212> TYPE: DNA <213> ORGANISM: Artificial Sequence <220> FEATURE:<223> OTHER INFORMATION: Restriction site <400> SEQUENCE: 12agctcggaat tccgagcttg gatcctctag agcggccgcc gactagtgag ct#cgtcgacc     60 cgggaatt                 #                  #                   #          68 <210> SEQ ID NO 13 <211> LENGTH: 68<212> TYPE: DNA <213> ORGANISM: Artificial Sequence <220> FEATURE:<223> OTHER INFORMATION: Restriction site <400> SEQUENCE: 13aattaattcc cgggtcgacg agctcactag tcggcggccg ctctagagga tc#caagctcg     60 gaattccg                 #                  #                   #          68 <210> SEQ ID NO 14 <211> LENGTH: 24<212> TYPE: DNA <213> ORGANISM: Artificial Sequence <220> FEATURE:<223> OTHER INFORMATION: Universal primer <400> SEQUENCE: 14agcggataac aatttcacac agga           #                  #                24 <210> SEQ ID NO 15 <211> LENGTH: 18 <212> TYPE: DNA<213> ORGANISM: Artificial Sequence <220> FEATURE:<223> OTHER INFORMATION: Universal primer <400> SEQUENCE: 15tgtaaaacga cggccagt              #                   #                  #  18 <210> SEQ ID NO 16 <211> LENGTH: 20 <212> TYPE: DNA<213> ORGANISM: Homo sapiens <400> SEQUENCE: 16ggaaatggtg tcccagttgc             #                  #                   # 20 <210> SEQ ID NO 17 <211> LENGTH: 20<212> TYPE: DNA <213> ORGANISM: Homo sapiens <400> SEQUENCE: 17tagcaagagc cacccaaacg             #                  #                   # 20 <210> SEQ ID NO 18 <211> LENGTH: 20<212> TYPE: DNA <213> ORGANISM: Homo sapiens <400> SEQUENCE: 18tcatcgaggt gtgtgttcgc             #                  #                   # 20 <210> SEQ ID NO 19 <211> LENGTH: 20<212> TYPE: DNA <213> ORGANISM: Homo sapiens <400> SEQUENCE: 19cgtctcctgc attctaagcg             #                  #                   # 20 <210> SEQ ID NO 20 <211> LENGTH: 20<212> TYPE: DNA <213> ORGANISM: Homo sapiens <400> SEQUENCE: 20cacagaatcc tgcgtgtgac             #                  #                   # 20 <210> SEQ ID NO 21 <211> LENGTH: 20<212> TYPE: DNA <213> ORGANISM: Homo sapiens <400> SEQUENCE: 21aggtcagcag caagttcacg             #                  #                   # 20 <210> SEQ ID NO 22 <211> LENGTH: 20<212> TYPE: DNA <213> ORGANISM: Homo sapiens <400> SEQUENCE: 22atcccatgta agccccgaat             #                  #                   # 20 <210> SEQ ID NO 23 <211> LENGTH: 302<212> TYPE: PRT <213> ORGANISM: Homo sapiens <400> SEQUENCE: 23Met Cys Ala Glu Arg Leu Gly Gln Phe Met Th #r Leu Ala Leu Val Leu 1               5   #                10   #                15Ala Thr Phe Asp Pro Ala Arg Gly Thr Asp Al #a Thr Asn Pro Pro Glu            20       #            25       #            30Gly Pro Gln Asp Arg Ser Ser Gln Gln Lys Gl #y Arg Leu Ser Leu Gln        35           #        40           #        45Asn Thr Ala Glu Ile Gln His Cys Leu Val As #n Ala Gly Asp Val Gly    50               #    55               #    60Cys Gly Val Phe Glu Cys Phe Glu Asn Asn Se #r Cys Glu Ile Arg Gly65                   #70                   #75                   #80Leu His Gly Ile Cys Met Thr Phe Leu His As #n Ala Gly Lys Phe Asp                85   #                90   #                95Ala Gln Gly Lys Ser Phe Ile Lys Asp Ala Le #u Lys Cys Lys Ala His            100       #           105       #           110Ala Leu Arg His Arg Phe Gly Cys Ile Ser Ar #g Lys Cys Pro Ala Ile        115           #       120           #       125Arg Glu Met Val Ser Gln Leu Gln Arg Glu Cy #s Tyr Leu Lys His Asp    130               #   135               #   140Leu Cys Ala Ala Ala Gln Glu Asn Thr Arg Va #l Ile Val Glu Met Ile145                 1 #50                 1 #55                 1 #60His Phe Lys Asp Leu Leu Leu His Glu Pro Ty #r Val Asp Leu Val Asn                165   #               170   #               175Leu Leu Leu Thr Cys Gly Glu Glu Val Lys Gl #u Ala Ile Thr His Ser            180       #           185       #           190Val Gln Val Gln Cys Glu Gln Asn Trp Gly Se #r Leu Cys Ser Ile Leu        195           #       200           #       205Ser Phe Cys Thr Ser Ala Ile Gln Lys Pro Pr #o Thr Ala Pro Pro Glu    210               #   215               #   220Arg Gln Pro Gln Val Asp Arg Thr Lys Leu Se #r Arg Ala His His Gly225                 2 #30                 2 #35                 2 #40Glu Ala Gly His His Leu Pro Glu Pro Ser Se #r Arg Glu Thr Gly Arg                245   #               250   #               255Gly Ala Lys Gly Glu Arg Gly Ser Lys Ser Hi #s Pro Asn Ala His Ala            260       #           265       #           270Arg Gly Arg Val Gly Gly Leu Gly Ala Gln Gl #y Pro Ser Gly Ser Ser        275           #       280           #       285Glu Trp Glu Asp Glu Gln Ser Glu Tyr Ser As #p Ile Arg Arg    290               #   295               #   300 <210> SEQ ID NO 24<211> LENGTH: 25 <212> TYPE: PRT <213> ORGANISM: Homo sapiens<400> SEQUENCE: 24 Leu Ser Arg Ala His His Gly Glu Ala Gly Hi#s His Leu Pro Glu Pro  1               5   #                10  #                15 Ser Ser Arg Glu Thr Gly Arg Gly Ala            20       #            25 <210> SEQ ID NO 25 <211> LENGTH: 23<212> TYPE: PRT <213> ORGANISM: Homo sapiens <400> SEQUENCE: 25Gly Ala Gln Gly Pro Ser Gly Ser Ser Glu Tr #p Glu Asp Glu Gln Ser 1               5   #                10   #                15Glu Tyr Ser Asp Ile Arg Arg             20 <210> SEQ ID NO 26<211> LENGTH: 20 <212> TYPE: PRT <213> ORGANISM: Homo sapiens<400> SEQUENCE: 26 Ala Ile Gln Lys Pro Pro Thr Ala Pro Pro Gl#u Arg Gln Pro Gln Val  1               5   #                10  #                15 Asp Arg Thr Lys             20 <210> SEQ ID NO 27<211> LENGTH: 20 <212> TYPE: PRT <213> ORGANISM: Homo sapiens<400> SEQUENCE: 27 Gln Asp Arg Ser Ser Gln Gln Lys Gly Arg Le#u Ser Leu Gln Asn Thr  1               5   #                10  #                15 Ala Glu Ile Gln             20 <210> SEQ ID NO 28<211> LENGTH: 8 <212> TYPE: PRT <213> ORGANISM: Artificial Sequence<220> FEATURE: <223> OTHER INFORMATION: Affinity purification system# recognition site <400> SEQUENCE: 28 Asp Tyr Lys Asp Asp Asp Asp Lys 1               5 <210> SEQ ID NO 29 <211> LENGTH: 21 <212> TYPE: PRT<213> ORGANISM: Artificial Sequence <220> FEATURE:<223> OTHER INFORMATION: Affinity purification system # recognition site<400> SEQUENCE: 29 Glu Gln Lys Leu Ile Ser Glu Glu Asp Leu As#n Met His Thr Glu His  1               5   #                10  #                15 His His His His His             20

We claim:
 1. A purified polynucleotide having a sequence selected fromthe group consisting of SEQUENCE ID NO:1, SEQUENCE ID NO:2, SEQUENCE IDNO:3, SEQUENCE ID NO:4, SEQUENCE ID NO:5, SEQUENCE ID NO:6, SEQUENCE IDNO:7, SEQUENCE ID NO:8, SEQUENCE ID NO:9, SEQUENCE ID NO:10, andSEQUENCE ID NO:11, full complements of SEQUENCE ID NO:1, SEQUENCE IDNO:2, SEQUENCE ID NO:3, SEQUENCE ID NO:4, SEQUENCE ID NO:5, SEQUENCE IDNO:6, SEQUENCE ID NO:7, SEQUENCE ID NO:8, SEQUENCE ID NO:9, SEQUENCE IDNO:10, and SEQUENCE ID NO:11, and equivalent degenerate coding sequencesthereof.
 2. The purified polynucleotide of claim 1 wherein saidpolynucleotide is produced by recombinant techniques.
 3. The purifiedpolynucleotide of claim 1 wherein said polynucleotide is produced bysynthetic techniques.
 4. A recombinant expression system comprising: anucleic acid sequence that includes an open reading frame operablylinked to a control sequence compatible with a desired host, the nucleicacid sequence selected from the group consisting of SEQUENCE ID NO:1,SEQUENCE ID NO:2, SEQUENCE ID NO:3, SEQUENCE ID NO:4, SEQUENCE ID NO:5,SEQUENCEID NO:6, SEQUENCE ID NO:7, SEQUENCE ID NO:8, SEQUENCE ID NO:9,SEQUENCE ID NO:10, and SEQUENCE ID NO:11, full complements of SEQUENCEID NO:1, SEQUENCE ID NO:2, SEQUENCE ID NO:3, SEQUENCE ID NO:4, SEQUENCEID NO:5, SEQUENCE ID NO:6, SEQUENCE ID NO:7, SEQUENCE ID NO:8, SEQUENCEID NO:9, SEQUENCE ID NO:10, and SEQUENCE ID NO:11, and equivalentdegenerate coding sequences thereof.
 5. A cell transfected with therecombinant expression system of claim
 4. 6. A cell transfected with anucleic acid sequence encoding at least one epitope, the nucleic acidsequence selected from the group consisting of SEQUENCE ID NO:1,SEQUENCE ID NO:2, SEQUENCE ID NO:3, SEQUENCE ID NO:4, SEQUENCE ID NO:5,SEQUENCE ID NO:6, SEQUENCE ID NO:7, SEQUENCE ID NO:8, SEQUENCE ID NO:9,SEQUENCE ID NO:10, and SEQUENCE ID NO:11, full complements of SEQUENCEID NO:1, SEQUENCE ID NO:2, SEQUENCE ID NO:3, SEQUENCE ID NO:4, SEQUENCEID NO:5, SEQUENCE ID NO:6, SEQUENCE ID NO:7, SEQUENCE ID NO:8, SEQUENCEID NO:9, SEQUENCE ID NO:10, and SEQUENCE ID NO:11, and equivalentdegenerate coding sequences thereof.
 7. An isolated protein comprisingan amino acid sequence of SEQUENCE ID NO:23.
 8. The isolated protein ofclaim 7 wherein said protein is produced by recombinant techniques. 9.The isolated of claim 7 wherein said protein is produced by synthetictechniques.
 10. An isolated polynucleotide comprising: DNA having asequence selected from the group consisting of SEQUENCE ID NO:10 andSEQUENCE ID NO:11, full complements of SEQUENCE ID NO:10 and SEQUENCE IDNO:11, and equivalent degenerate coding sequences thereof.
 11. Theisolated polynucleotide of claim 10 wherein said polynucleotide isproduced by recombinant techniques.
 12. The isolated polynucleotide ofclaim 10 wherein said polynucleotide is produced by synthetictechniques.